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dealii.git
6 years agoMerge pull request #6408 from bangerth/step-51
Wolfgang Bangerth [Thu, 3 May 2018 00:31:25 +0000 (18:31 -0600)]
Merge pull request #6408 from bangerth/step-51

Minor edits to the step-51 introduction.

6 years agoMinor edits to the step-51 introduction. 6408/head
Wolfgang Bangerth [Tue, 1 May 2018 04:26:14 +0000 (22:26 -0600)]
Minor edits to the step-51 introduction.

Specifically, make sure 'FE_DGPMonomial' is spelled correctly. While there,
also address a couple of other things.

6 years agoMerge pull request #6426 from drwells/fix-clang-6-warnings
Daniel Arndt [Wed, 2 May 2018 23:14:29 +0000 (01:14 +0200)]
Merge pull request #6426 from drwells/fix-clang-6-warnings

Fix clang 6 warnings

6 years agoMerge pull request #6420 from masterleinad/update_base_assign_subscriptor
David Wells [Wed, 2 May 2018 19:18:03 +0000 (15:18 -0400)]
Merge pull request #6420 from masterleinad/update_base_assign_subscriptor

Update test output for base/assign_subscriptor without threads

6 years agoRemoved an unused typedef. 6426/head
David Wells [Wed, 2 May 2018 19:12:43 +0000 (15:12 -0400)]
Removed an unused typedef.

6 years agoUse nullptr instead of 0.
David Wells [Wed, 2 May 2018 19:12:40 +0000 (15:12 -0400)]
Use nullptr instead of 0.

6 years agoMerge pull request #6424 from tamiko/fix_mpi_version_variables_2
Denis Davydov [Wed, 2 May 2018 18:10:25 +0000 (20:10 +0200)]
Merge pull request #6424 from tamiko/fix_mpi_version_variables_2

CMake: Fix MPI version detection, round two

6 years agoCMake: Fix MPI version detection, round two 6424/head
Matthias Maier [Wed, 2 May 2018 14:35:48 +0000 (09:35 -0500)]
CMake: Fix MPI version detection, round two

6 years agoMerge pull request #6421 from tamiko/fix_mpi_version_variables
Martin Kronbichler [Wed, 2 May 2018 12:08:30 +0000 (14:08 +0200)]
Merge pull request #6421 from tamiko/fix_mpi_version_variables

CMake: Fix MPI version detection for newer cmake

6 years agoMerge pull request #6390 from masterleinad/new_fixes_4
Martin Kronbichler [Wed, 2 May 2018 07:07:32 +0000 (09:07 +0200)]
Merge pull request #6390 from masterleinad/new_fixes_4

Provide alternative output for the *vector_add_and_dot_complex tests without threads

6 years agoMerge pull request #6418 from masterleinad/update_lac_vector_memory
Martin Kronbichler [Wed, 2 May 2018 05:53:55 +0000 (07:53 +0200)]
Merge pull request #6418 from masterleinad/update_lac_vector_memory

Update alternative test output for lac/vector_memory

6 years agoMerge pull request #6417 from kkormann/fix_6300
Daniel Arndt [Wed, 2 May 2018 00:08:32 +0000 (02:08 +0200)]
Merge pull request #6417 from kkormann/fix_6300

Fix matrix-free commits (comments by Bruno Turcksin).

6 years agoCMake: Fix MPI version detection for newer cmake 6421/head
Matthias Maier [Tue, 1 May 2018 23:39:02 +0000 (18:39 -0500)]
CMake: Fix MPI version detection for newer cmake

6 years agoCMake: Remove OpenMPI specific version detection
Matthias Maier [Tue, 1 May 2018 23:30:39 +0000 (18:30 -0500)]
CMake: Remove OpenMPI specific version detection

6 years agoUpdate test output for base/assign_subscriptor without threads 6420/head
Daniel Arndt [Tue, 1 May 2018 23:14:44 +0000 (01:14 +0200)]
Update test output for base/assign_subscriptor without threads

6 years agoMerge pull request #6419 from masterleinad/update_base_reference
David Wells [Tue, 1 May 2018 23:09:31 +0000 (19:09 -0400)]
Merge pull request #6419 from masterleinad/update_base_reference

Update test output for base/reference without threads

6 years agoUpdate test output for base/reference without threads 6419/head
Daniel Arndt [Tue, 1 May 2018 23:04:32 +0000 (01:04 +0200)]
Update test output for base/reference without threads

6 years agoUpdate alternative test output for lac/vector_memory 6418/head
Daniel Arndt [Tue, 1 May 2018 22:47:40 +0000 (00:47 +0200)]
Update alternative test output for lac/vector_memory

6 years agoMerge pull request #6405 from masterleinad/undefined_4
Daniel Arndt [Tue, 1 May 2018 21:47:47 +0000 (23:47 +0200)]
Merge pull request #6405 from masterleinad/undefined_4

Avoid accessing elements of a zero size vector in ParticleHandler

6 years agoFix matrix-free commits (comments by Bruno Turcksin). 6417/head
Katharina Kormann [Tue, 1 May 2018 20:32:51 +0000 (22:32 +0200)]
Fix matrix-free commits (comments by Bruno Turcksin).

6 years agoMerge pull request #6414 from kronbichler/issue_6403
Daniel Arndt [Tue, 1 May 2018 19:54:58 +0000 (21:54 +0200)]
Merge pull request #6414 from kronbichler/issue_6403

Use std::vector::data+offset() rather than [] access

6 years agoMerge pull request #6413 from masterleinad/undefined_8
Wolfgang Bangerth [Tue, 1 May 2018 17:33:12 +0000 (11:33 -0600)]
Merge pull request #6413 from masterleinad/undefined_8

Avoid creating pointer to invalid memory in get_dof_indices

6 years agoMerge pull request #6409 from bangerth/add-include
David Wells [Tue, 1 May 2018 17:06:32 +0000 (13:06 -0400)]
Merge pull request #6409 from bangerth/add-include

Add a necessary #include file.

6 years agoRemove unnecessary const_cast. 6414/head
Martin Kronbichler [Tue, 1 May 2018 16:21:45 +0000 (18:21 +0200)]
Remove unnecessary const_cast.

6 years agoMerge pull request #6412 from masterleinad/initialize_sun
Luca Heltai [Tue, 1 May 2018 15:29:27 +0000 (17:29 +0200)]
Merge pull request #6412 from masterleinad/initialize_sun

Initialize SUN* objects

6 years agoMerge pull request #6381 from drwells/update-step-6
Luca Heltai [Tue, 1 May 2018 14:32:29 +0000 (16:32 +0200)]
Merge pull request #6381 from drwells/update-step-6

Update step 6.

6 years agoUse vector::data() + offset in a few places. Add assertion.
Martin Kronbichler [Tue, 1 May 2018 13:07:35 +0000 (15:07 +0200)]
Use vector::data() + offset in a few places. Add assertion.

6 years agoDo not dereference pointers as we might be at the end of the array.
Martin Kronbichler [Tue, 1 May 2018 13:06:53 +0000 (15:06 +0200)]
Do not dereference pointers as we might be at the end of the array.

6 years agoSimplify the last AssertThrow 6405/head
Daniel Arndt [Tue, 1 May 2018 10:54:15 +0000 (12:54 +0200)]
Simplify the last AssertThrow

6 years agoAvoid accessing elements of a zero size vector in ParticleHandler
Daniel Arndt [Mon, 30 Apr 2018 16:46:43 +0000 (18:46 +0200)]
Avoid accessing elements of a zero size vector in ParticleHandler

6 years agoAvoid creating pointer to invalid memory in get_dof_indices 6413/head
Daniel Arndt [Tue, 1 May 2018 09:58:32 +0000 (11:58 +0200)]
Avoid creating pointer to invalid memory in get_dof_indices

6 years agoInitialize SUN* objects 6412/head
Daniel Arndt [Tue, 1 May 2018 09:01:24 +0000 (11:01 +0200)]
Initialize SUN* objects

6 years agoMerge pull request #6404 from masterleinad/undefined_3
Daniel Arndt [Tue, 1 May 2018 09:04:06 +0000 (11:04 +0200)]
Merge pull request #6404 from masterleinad/undefined_3

Guard accessing values in Vector<Number>::zero_out_ghosts

6 years agoAdd a necessary #include file. 6409/head
Wolfgang Bangerth [Tue, 1 May 2018 04:28:01 +0000 (22:28 -0600)]
Add a necessary #include file.

We now reference the 'free' function in the .h file. We need to '#include' the necessary
header file.

6 years agoMerge pull request #6401 from masterleinad/undefined_1
Wolfgang Bangerth [Tue, 1 May 2018 04:12:39 +0000 (22:12 -0600)]
Merge pull request #6401 from masterleinad/undefined_1

Only invert bits up to the maximum possible in ~CacheUpdateFlags

6 years agoMerge pull request #6406 from masterleinad/undefined_5
Wolfgang Bangerth [Tue, 1 May 2018 04:04:41 +0000 (22:04 -0600)]
Merge pull request #6406 from masterleinad/undefined_5

Avoid signed overflow in test

6 years agoMerge pull request #6402 from masterleinad/undefined_2
Wolfgang Bangerth [Tue, 1 May 2018 04:02:01 +0000 (22:02 -0600)]
Merge pull request #6402 from masterleinad/undefined_2

Avoid signed overflow in Testing::rand

6 years agoMerge pull request #6387 from masterleinad/correct_deleter_readwritevector_values
Wolfgang Bangerth [Tue, 1 May 2018 03:50:11 +0000 (21:50 -0600)]
Merge pull request #6387 from masterleinad/correct_deleter_readwritevector_values

Call the correct deleter for ReadWriteVector::values

6 years agoChange style of array access 6404/head
Daniel Arndt [Mon, 30 Apr 2018 23:24:30 +0000 (01:24 +0200)]
Change style of array access

6 years agoFix some documentation regarding exception handling. 6381/head
David Wells [Mon, 30 Apr 2018 22:11:08 +0000 (18:11 -0400)]
Fix some documentation regarding exception handling.

6 years agoAvoid signed overflow in test 6406/head
Daniel Arndt [Mon, 30 Apr 2018 20:36:42 +0000 (22:36 +0200)]
Avoid signed overflow in test

6 years agoMerge pull request #6371 from jppelteret/follow_up_to_6335-2
David Wells [Mon, 30 Apr 2018 19:34:31 +0000 (15:34 -0400)]
Merge pull request #6371 from jppelteret/follow_up_to_6335-2

CMake: Make Adol-C check for boost pool more specific.

6 years agoMerge pull request #6398 from davydden/tests/zoltan
David Wells [Mon, 30 Apr 2018 19:25:37 +0000 (15:25 -0400)]
Merge pull request #6398 from davydden/tests/zoltan

zoltan: run with mpirun annotation to avoid race condition

6 years agoMerge pull request #6263 from mathgirl/assert_in_do_integrate_difference
David Wells [Mon, 30 Apr 2018 19:18:43 +0000 (15:18 -0400)]
Merge pull request #6263 from mathgirl/assert_in_do_integrate_difference

Add missing assert in do_integrate_difference

6 years agoMerge pull request #6391 from masterleinad/new_fixes_3
David Wells [Mon, 30 Apr 2018 18:47:10 +0000 (14:47 -0400)]
Merge pull request #6391 from masterleinad/new_fixes_3

Avoid accessing invalid memory in base/utilities_pack_unpack_04

6 years agoMerge pull request #6399 from GivAlz/NonMatchDocu
David Wells [Mon, 30 Apr 2018 17:37:19 +0000 (13:37 -0400)]
Merge pull request #6399 from GivAlz/NonMatchDocu

Fix documentation for NonMatching

6 years agoMerge pull request #6392 from masterleinad/new_fixes_2
David Wells [Mon, 30 Apr 2018 17:36:04 +0000 (13:36 -0400)]
Merge pull request #6392 from masterleinad/new_fixes_2

Clarify that base/reference causes stack-use-after-scope

6 years agoMerge pull request #6375 from masterleinad/fix_scalapack_create_group
Timo Heister [Mon, 30 Apr 2018 17:32:26 +0000 (13:32 -0400)]
Merge pull request #6375 from masterleinad/fix_scalapack_create_group

Fix scalapack create group

6 years agoGuard accessing values in Vector<Number>::zero_out_ghosts
Daniel Arndt [Mon, 30 Apr 2018 16:35:24 +0000 (18:35 +0200)]
Guard accessing values in Vector<Number>::zero_out_ghosts

6 years agoAdd documentation to nonoverflow_add 6402/head
Daniel Arndt [Mon, 30 Apr 2018 16:16:11 +0000 (18:16 +0200)]
Add documentation to nonoverflow_add

6 years agoAdded documentation for NonMatching namespace 6399/head
Giovanni Alzetta [Mon, 30 Apr 2018 12:45:02 +0000 (14:45 +0200)]
Added documentation for NonMatching namespace

6 years agoAvoid signed overflow in Testing::rand
Daniel Arndt [Mon, 30 Apr 2018 15:36:50 +0000 (17:36 +0200)]
Avoid signed overflow in Testing::rand

6 years agoOnly invert bits up to the maximum possible in ~CacheUpdateFlags 6401/head
Daniel Arndt [Mon, 30 Apr 2018 15:27:28 +0000 (17:27 +0200)]
Only invert bits up to the maximum possible in ~CacheUpdateFlags

6 years agoMerge pull request #6400 from drwells/remove-double-stars
Denis Davydov [Mon, 30 Apr 2018 13:38:08 +0000 (15:38 +0200)]
Merge pull request #6400 from drwells/remove-double-stars

Avoid using '**/' at the end of comments.

6 years agoAvoid using '**/' at the end of comments. 6400/head
David Wells [Mon, 30 Apr 2018 13:09:25 +0000 (09:09 -0400)]
Avoid using '**/' at the end of comments.

6 years agozoltan: run with mpirun annotation to avoid race condition 6398/head
Denis Davydov [Mon, 30 Apr 2018 12:40:41 +0000 (14:40 +0200)]
zoltan: run with mpirun annotation to avoid race condition

6 years agoMerge pull request #6395 from kronbichler/test_fixes_avx512
Martin Kronbichler [Mon, 30 Apr 2018 12:14:09 +0000 (14:14 +0200)]
Merge pull request #6395 from kronbichler/test_fixes_avx512

Test fixes with AVX-512

6 years agoMerge pull request #6296 from luca-heltai/failing-test
Daniel Arndt [Mon, 30 Apr 2018 10:10:29 +0000 (12:10 +0200)]
Merge pull request #6296 from luca-heltai/failing-test

Fix bug in MappingFEField

6 years agoMerge pull request #6389 from masterleinad/fix_memory_leak_kinsol
Denis Davydov [Mon, 30 Apr 2018 09:42:12 +0000 (11:42 +0200)]
Merge pull request #6389 from masterleinad/fix_memory_leak_kinsol

Fix memory leak in KINSOL wrapper

6 years agoTest fixes with AVX-512. 6395/head
Martin Kronbichler [Mon, 30 Apr 2018 08:55:54 +0000 (10:55 +0200)]
Test fixes with AVX-512.

6 years agoClarify that base/reference causes stack-use-after-scope 6392/head
Daniel Arndt [Sun, 29 Apr 2018 23:10:45 +0000 (01:10 +0200)]
Clarify that base/reference causes stack-use-after-scope

6 years agoAvoid accessing invalid memory in base/utilities_pack_unpack_04 6391/head
Daniel Arndt [Sun, 29 Apr 2018 23:11:36 +0000 (01:11 +0200)]
Avoid accessing invalid memory in base/utilities_pack_unpack_04

6 years agoProvide alternative output for the *vector_add_and_dot_complex tests without threads 6390/head
Daniel Arndt [Sun, 29 Apr 2018 23:13:19 +0000 (01:13 +0200)]
Provide alternative output for the *vector_add_and_dot_complex tests without threads

6 years agoFix memory leak in KINSOL wrapper 6389/head
Daniel Arndt [Sun, 29 Apr 2018 21:04:42 +0000 (23:04 +0200)]
Fix memory leak in KINSOL wrapper

6 years agoUse initializer list instead of default initializer 6387/head
Daniel Arndt [Sun, 29 Apr 2018 20:49:20 +0000 (22:49 +0200)]
Use initializer list instead of default initializer

6 years agoMerge pull request #6388 from kronbichler/documentation_matrix_free
Bruno Turcksin [Sun, 29 Apr 2018 19:31:54 +0000 (15:31 -0400)]
Merge pull request #6388 from kronbichler/documentation_matrix_free

Improve documentation of new matrix free data structures

6 years agoMerge pull request #6385 from masterleinad/fix_warning_nonconst_comparator
Martin Kronbichler [Sun, 29 Apr 2018 16:04:43 +0000 (18:04 +0200)]
Merge pull request #6385 from masterleinad/fix_warning_nonconst_comparator

Fix warning for non-const comparator

6 years agoMerge pull request #6386 from kronbichler/mf_face_emplace_back
Martin Kronbichler [Sun, 29 Apr 2018 14:49:45 +0000 (16:49 +0200)]
Merge pull request #6386 from kronbichler/mf_face_emplace_back

Prefer emplace_back over push_back in a few places

6 years agoDocument new parameters. 6388/head
Martin Kronbichler [Sun, 29 Apr 2018 14:25:36 +0000 (16:25 +0200)]
Document new parameters.

6 years agoFix doxygen appearance of MatrixFree::Loop.
Martin Kronbichler [Sun, 29 Apr 2018 14:24:59 +0000 (16:24 +0200)]
Fix doxygen appearance of MatrixFree::Loop.

6 years agoFix copydoc in FEEvaluationBase.
Martin Kronbichler [Sun, 29 Apr 2018 14:24:24 +0000 (16:24 +0200)]
Fix copydoc in FEEvaluationBase.

6 years agoCall the correct deleter for ReadWriteVector::values
Daniel Arndt [Sun, 29 Apr 2018 13:14:06 +0000 (15:14 +0200)]
Call the correct deleter for ReadWriteVector::values

6 years agoMerge pull request #6368 from drwells/fix-assert-nothrow-slicing
Daniel Arndt [Sun, 29 Apr 2018 12:12:07 +0000 (14:12 +0200)]
Merge pull request #6368 from drwells/fix-assert-nothrow-slicing

Fix assert nothrow slicing

6 years agoPrefer emplace_back over push_back in a few places. 6386/head
Martin Kronbichler [Sun, 29 Apr 2018 11:06:22 +0000 (13:06 +0200)]
Prefer emplace_back over push_back in a few places.

6 years agoFix warning for non-const comparator 6385/head
Daniel Arndt [Sun, 29 Apr 2018 10:16:12 +0000 (12:16 +0200)]
Fix warning for non-const comparator

6 years agoMerge pull request #6384 from kronbichler/fix_changelog
Jean-Paul Pelteret [Sun, 29 Apr 2018 10:05:32 +0000 (12:05 +0200)]
Merge pull request #6384 from kronbichler/fix_changelog

Break lines before author names in changelog

6 years agoBreak lines before author names in changelog. 6384/head
Martin Kronbichler [Sun, 29 Apr 2018 10:02:31 +0000 (12:02 +0200)]
Break lines before author names in changelog.

6 years agoLink p4est issue in 6375/head
Daniel Arndt [Sun, 29 Apr 2018 09:48:03 +0000 (11:48 +0200)]
Link p4est issue in

6 years agoChangelog entry
Daniel Arndt [Sat, 28 Apr 2018 17:54:09 +0000 (19:54 +0200)]
Changelog entry

6 years agoAdd test
Daniel Arndt [Sat, 28 Apr 2018 17:48:17 +0000 (19:48 +0200)]
Add test

6 years agoUse Utilities::MPI::MPI_Comm_create_group
Daniel Arndt [Sat, 28 Apr 2018 12:21:13 +0000 (14:21 +0200)]
Use Utilities::MPI::MPI_Comm_create_group

6 years agoAdd Utilities::MPI::MPI_Comm_create_group
Daniel Arndt [Sat, 28 Apr 2018 12:18:54 +0000 (14:18 +0200)]
Add Utilities::MPI::MPI_Comm_create_group

6 years agoAdd MPI version check
Daniel Arndt [Sat, 28 Apr 2018 12:17:26 +0000 (14:17 +0200)]
Add MPI version check

6 years agoMerge pull request #6377 from kronbichler/matrix_free_fixes
Martin Kronbichler [Sun, 29 Apr 2018 06:19:19 +0000 (08:19 +0200)]
Merge pull request #6377 from kronbichler/matrix_free_fixes

Matrix free DG test fixes

6 years agoMerge pull request #6382 from drwells/remove-more-c++11-references
Denis Davydov [Sun, 29 Apr 2018 05:01:28 +0000 (07:01 +0200)]
Merge pull request #6382 from drwells/remove-more-c++11-references

Remove some references to C++11 support.

6 years agoMerge pull request #6383 from drwells/fix-doc-typos-9
Denis Davydov [Sun, 29 Apr 2018 04:55:04 +0000 (06:55 +0200)]
Merge pull request #6383 from drwells/fix-doc-typos-9

Fix more typos.

6 years agoMerge pull request #6380 from masterleinad/disable_sc_init
David Wells [Sun, 29 Apr 2018 02:17:30 +0000 (22:17 -0400)]
Merge pull request #6380 from masterleinad/disable_sc_init

Disable sc_init

6 years agoFix more typos. 6383/head
David Wells [Sun, 29 Apr 2018 01:26:34 +0000 (21:26 -0400)]
Fix more typos.

Work was done by codespell and the (newly fixed) double_word_typos.py script.

6 years agoRemove some references to C++11 support. 6382/head
David Wells [Sun, 29 Apr 2018 00:39:43 +0000 (20:39 -0400)]
Remove some references to C++11 support.

6 years agoMerge pull request #6379 from drwells/no-subscripers-noexcept
Daniel Arndt [Sat, 28 Apr 2018 23:31:14 +0000 (01:31 +0200)]
Merge pull request #6379 from drwells/no-subscripers-noexcept

Mark Subscriptor::check_no_subscribers as noexcept.

6 years agoEdit some documentation in step-6 for clarity.
David Wells [Sat, 28 Apr 2018 22:17:28 +0000 (18:17 -0400)]
Edit some documentation in step-6 for clarity.

6 years agoClean up the headers in step-6.
David Wells [Sat, 28 Apr 2018 16:08:51 +0000 (12:08 -0400)]
Clean up the headers in step-6.

6 years agoRemove trailing spaces in step-6.
David Wells [Sat, 28 Apr 2018 21:30:09 +0000 (17:30 -0400)]
Remove trailing spaces in step-6.

6 years agoUpdate images in step-6.
David Wells [Sat, 28 Apr 2018 21:39:29 +0000 (17:39 -0400)]
Update images in step-6.

6 years agoFix the remaining tests 6263/head
Daniel Arndt [Sat, 28 Apr 2018 21:54:37 +0000 (23:54 +0200)]
Fix the remaining tests

6 years agoRedo the SmartPointer description in step-6.
David Wells [Sat, 28 Apr 2018 21:37:34 +0000 (17:37 -0400)]
Redo the SmartPointer description in step-6.

The old version doesn't make sense anymore since a Triangulation does not store
a SmartPointer pointing to a manifold.

6 years agoRemove explicit manifold usage from step-6.
David Wells [Sat, 28 Apr 2018 21:35:05 +0000 (17:35 -0400)]
Remove explicit manifold usage from step-6.

6 years agoMerge pull request #6378 from kronbichler/fix_vectorized_scatter
Daniel Arndt [Sat, 28 Apr 2018 21:01:11 +0000 (23:01 +0200)]
Merge pull request #6378 from kronbichler/fix_vectorized_scatter

Fix vectorized scatter for AVX-512

6 years agoDisable sc_init 6380/head
Daniel Arndt [Sat, 28 Apr 2018 20:33:44 +0000 (22:33 +0200)]
Disable sc_init

6 years agoMark Subscriptor::check_no_subscribers as noexcept. 6379/head
David Wells [Sat, 28 Apr 2018 16:49:05 +0000 (12:49 -0400)]
Mark Subscriptor::check_no_subscribers as noexcept.

Follow-up to a029a7f7acb7fe1a9bd30672b23da577af3c1932: since this function
should never throw we can mark it as noexcept.

This commit also updates relevant documentation explaining the present
behavior.


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