]> https://gitweb.dealii.org/ - dealii.git/log
dealii.git
6 years agoAvoid \0 delimeter
Matthias Maier [Fri, 15 Jun 2018 05:20:49 +0000 (00:20 -0500)]
Avoid \0 delimeter

We actually do not need any \0 delimeter because '\n' is an invalid
character in file names. So, simply switch to '\n' delimeted output.
This helps with Mac OS X compatibility because there grep might not have
the -z (--null-data) option and can thus not correctly match null
terminated input...

6 years agoAdd script that reindents recently changed files.
David Wells [Fri, 25 May 2018 21:29:48 +0000 (17:29 -0400)]
Add script that reindents recently changed files.

My laptop needs about 30s to run clang-format since the script currently
reindents all files regardless of whether or not they have been
modified. This PR adds a new target indent-branch that only reindents
files that have been modified (or added) since the last commit to
master. This takes less than a second to run (with a few files changed)
on my laptop.

6 years agoMerge pull request #6762 from tamiko/improve_indent_script
Wolfgang Bangerth [Thu, 14 Jun 2018 23:46:54 +0000 (17:46 -0600)]
Merge pull request #6762 from tamiko/improve_indent_script

contrib/utilities/indent: Reorganize script

6 years agomake Mac OSX's sed happy 6762/head
Matthias Maier [Thu, 14 Jun 2018 23:39:37 +0000 (18:39 -0500)]
make Mac OSX's sed happy

6 years agorun indent script
Matthias Maier [Thu, 14 Jun 2018 22:55:12 +0000 (17:55 -0500)]
run indent script

6 years agoimprove error messages
Matthias Maier [Thu, 14 Jun 2018 23:04:47 +0000 (18:04 -0500)]
improve error messages

6 years agoDo not change line ending in output files
Matthias Maier [Thu, 14 Jun 2018 22:44:40 +0000 (17:44 -0500)]
Do not change line ending in output files

Some of the output files are binary files, we shouldn't touch them.

6 years agocontrib/utilities/indent: Reorganize script
Matthias Maier [Thu, 14 Jun 2018 20:02:39 +0000 (15:02 -0500)]
contrib/utilities/indent: Reorganize script

This commit

 - reorganizes the core indenting logic into a indent_common.sh file

 - cleans up find and indenting logic to make everything more readable

 - prepares for more specialized indent versions (see #6673)

6 years agoMerge pull request #6757 from piyueh/fix#6756
Matthias Maier [Thu, 14 Jun 2018 21:33:35 +0000 (16:33 -0500)]
Merge pull request #6757 from piyueh/fix#6756

Fix #6756

6 years agoMerge pull request #6746 from masterleinad/deprecate_function_map
Matthias Maier [Thu, 14 Jun 2018 21:19:47 +0000 (16:19 -0500)]
Merge pull request #6746 from masterleinad/deprecate_function_map

Deprecate FunctionMap

6 years agoMerge branch 'master' into fix#6756 6757/head
Daniel Arndt [Thu, 14 Jun 2018 21:14:12 +0000 (23:14 +0200)]
Merge branch 'master' into fix#6756

6 years agoMerge pull request #6755 from tamiko/clang_format_struck_again
Wolfgang Bangerth [Thu, 14 Jun 2018 21:13:28 +0000 (15:13 -0600)]
Merge pull request #6755 from tamiko/clang_format_struck_again

Headline: clang-format struck again

6 years agolog the changes to doc/news/changes/minor
Pi-Yueh Chuang [Thu, 14 Jun 2018 18:15:29 +0000 (14:15 -0400)]
log the changes to doc/news/changes/minor

6 years agorun indent script to follow the coding format
Pi-Yueh Chuang [Thu, 14 Jun 2018 04:49:20 +0000 (00:49 -0400)]
run indent script to follow the coding format

6 years agofix #6756
Pi-Yueh Chuang [Thu, 14 Jun 2018 00:34:12 +0000 (20:34 -0400)]
fix #6756

6 years agoExamples: Add updated comment pragma regex to examples directory 6755/head
Matthias Maier [Wed, 13 Jun 2018 19:43:55 +0000 (14:43 -0500)]
Examples: Add updated comment pragma regex to examples directory

This isn't really necessary (no indenting changes) but it doesn't hurt.

6 years agoFix broken doxygen formatting
Matthias Maier [Wed, 13 Jun 2018 19:13:43 +0000 (14:13 -0500)]
Fix broken doxygen formatting

6 years agoBugfix: list *all* doxygen formatting options as comment pragmas
Matthias Maier [Wed, 13 Jun 2018 19:14:10 +0000 (14:14 -0500)]
Bugfix: list *all* doxygen formatting options as comment pragmas

This way clang-format will keep any comment line that contains such a
symbol untouched. Otherwise we are garbling up way too many doxygen
pragmas...

6 years agoMerge branch 'master' into deprecate_function_map 6746/head
Daniel Arndt [Thu, 14 Jun 2018 16:15:18 +0000 (18:15 +0200)]
Merge branch 'master' into deprecate_function_map

6 years agoMerge pull request #6758 from tamiko/remove_string_literal
Daniel Arndt [Thu, 14 Jun 2018 15:06:48 +0000 (17:06 +0200)]
Merge pull request #6758 from tamiko/remove_string_literal

fe/fe_nothing.cc: put a string literal where it belongs

6 years agofe/fe_nothing.cc: put a string literal where it belongs 6758/head
Matthias Maier [Thu, 14 Jun 2018 01:04:06 +0000 (20:04 -0500)]
fe/fe_nothing.cc: put a string literal where it belongs

6 years agoChangelog entry
Daniel Arndt [Mon, 11 Jun 2018 15:47:34 +0000 (17:47 +0200)]
Changelog entry

6 years agoAvoid FunctionMap in tests
Daniel Arndt [Mon, 11 Jun 2018 15:28:50 +0000 (17:28 +0200)]
Avoid FunctionMap in tests

6 years agoAvoid FunctionMap in code base
Daniel Arndt [Mon, 11 Jun 2018 14:53:59 +0000 (16:53 +0200)]
Avoid FunctionMap in code base

6 years agoDeprecate FunctionMap
Daniel Arndt [Mon, 11 Jun 2018 10:37:21 +0000 (12:37 +0200)]
Deprecate FunctionMap

6 years agoMerge pull request #6696 from tamiko/improve-clang-format
Wolfgang Bangerth [Thu, 14 Jun 2018 05:50:57 +0000 (23:50 -0600)]
Merge pull request #6696 from tamiko/improve-clang-format

tweak clang-format configuration

6 years agorun indent 6696/head
Matthias Maier [Wed, 13 Jun 2018 19:55:40 +0000 (14:55 -0500)]
run indent

6 years agotweak .clang-format file
Matthias Maier [Wed, 30 May 2018 01:34:06 +0000 (20:34 -0500)]
tweak .clang-format file

6 years agoMerge pull request #6753 from tjhei/doxygen_formatting_fixes
Matthias Maier [Wed, 13 Jun 2018 18:50:14 +0000 (13:50 -0500)]
Merge pull request #6753 from tjhei/doxygen_formatting_fixes

fix doxygen formatting errors

6 years agofix doxygen formatting errors 6753/head
Timo Heister [Wed, 13 Jun 2018 18:43:46 +0000 (14:43 -0400)]
fix doxygen formatting errors

6 years agoMerge pull request #6748 from davydden/bugfix/mf_ghosts_and_block_vectors
Martin Kronbichler [Wed, 13 Jun 2018 12:56:28 +0000 (14:56 +0200)]
Merge pull request #6748 from davydden/bugfix/mf_ghosts_and_block_vectors

fixed a bug where exchanger.ghosts_were_set was not set for vectors …

6 years agoMerge pull request #6749 from masterleinad/fe_face_evaluation_deg-1
Martin Kronbichler [Wed, 13 Jun 2018 12:53:12 +0000 (14:53 +0200)]
Merge pull request #6749 from masterleinad/fe_face_evaluation_deg-1

Allow using FEFaceEvaluation with degree=-1

6 years agoMerge pull request #6694 from davydden/feature/timer_output_combine
Denis Davydov [Wed, 13 Jun 2018 09:20:19 +0000 (11:20 +0200)]
Merge pull request #6694 from davydden/feature/timer_output_combine

combine CPU and wallclock tables in TimerOutput

6 years agoMark variables as constexpr 6749/head
Daniel Arndt [Wed, 13 Jun 2018 08:13:03 +0000 (10:13 +0200)]
Mark variables as constexpr

6 years agoremove redundant setw() and setprecision() 6694/head
Denis Davydov [Wed, 13 Jun 2018 05:55:26 +0000 (07:55 +0200)]
remove redundant setw() and setprecision()

6 years agoAllow using FEFaceEvaluation with degree=-1
Daniel Arndt [Tue, 12 Jun 2018 22:48:33 +0000 (00:48 +0200)]
Allow using FEFaceEvaluation with degree=-1

6 years agouse range-based loops
Denis Davydov [Tue, 12 Jun 2018 20:52:03 +0000 (22:52 +0200)]
use range-based loops

6 years agominor cleanup
Denis Davydov [Tue, 12 Jun 2018 20:44:50 +0000 (22:44 +0200)]
minor cleanup

6 years agoadd dealii::BlockVector::has_ghost_elements() 6748/head
Denis Davydov [Tue, 12 Jun 2018 20:28:51 +0000 (22:28 +0200)]
add dealii::BlockVector::has_ghost_elements()

6 years agoMerge pull request #6738 from masterleinad/restrict_thread_tests
Matthias Maier [Tue, 12 Jun 2018 16:45:32 +0000 (11:45 -0500)]
Merge pull request #6738 from masterleinad/restrict_thread_tests

Restrict tests that require DEAL_II_WITH_THREADS=ON

6 years agoMerge pull request #6736 from masterleinad/restrict_clang_tidy
Matthias Maier [Tue, 12 Jun 2018 16:45:02 +0000 (11:45 -0500)]
Merge pull request #6736 from masterleinad/restrict_clang_tidy

Restrict directories to apply clang-format to

6 years agoMerge pull request #6742 from masterleinad/fix_identical_block_linear_operator
Matthias Maier [Tue, 12 Jun 2018 16:43:59 +0000 (11:43 -0500)]
Merge pull request #6742 from masterleinad/fix_identical_block_linear_operator

BlockLinearOperator: Allow identical destination and source

6 years agoMerge pull request #6741 from masterleinad/add_codecov_configuration
Matthias Maier [Tue, 12 Jun 2018 16:43:40 +0000 (11:43 -0500)]
Merge pull request #6741 from masterleinad/add_codecov_configuration

Add codecov configuration

6 years agoreturn from reset_ghost_values() immediately if exchanger.ghosts_were_set == true
Denis Davydov [Tue, 12 Jun 2018 14:21:45 +0000 (16:21 +0200)]
return from reset_ghost_values() immediately if exchanger.ghosts_were_set == true

6 years agofixed a bug where exchanger.ghosts_were_set was not set
Denis Davydov [Tue, 12 Jun 2018 13:30:33 +0000 (15:30 +0200)]
fixed a bug where exchanger.ghosts_were_set was not set
for vectors with large number of blocks. Update the test
to make sure this is being checked.

6 years agoMerge pull request #6739 from masterleinad/alternative_pack_unpack
Timo Heister [Tue, 12 Jun 2018 13:28:29 +0000 (09:28 -0400)]
Merge pull request #6739 from masterleinad/alternative_pack_unpack

Alternative output for base/utilities_pack_unpack_06

6 years agoMerge pull request #6745 from tamiko/fix_insource_builds
Timo Heister [Tue, 12 Jun 2018 02:16:54 +0000 (10:16 +0800)]
Merge pull request #6745 from tamiko/fix_insource_builds

CMake: Fix in-source builds

6 years agoMove helper functions into anonymous namespace 6742/head
Daniel Arndt [Mon, 11 Jun 2018 16:50:31 +0000 (18:50 +0200)]
Move helper functions into anonymous namespace

6 years agodoc: add a news item 6745/head
Matthias Maier [Mon, 11 Jun 2018 16:07:21 +0000 (11:07 -0500)]
doc: add a news item

6 years agoCMake: Fix insource builds
Matthias Maier [Mon, 11 Jun 2018 15:54:55 +0000 (10:54 -0500)]
CMake: Fix insource builds

In case of an in-source build (which we officially support)
CMAKE_BINARY_DIR==CMAKE_SOURCE_DIR. With that, the boost test fails (by
brutally removing its own source directory...)

Fix this by using a different name for the working directory

6 years agoMerge pull request #6715 from dsambit/scalapackWrapperTriangularMatInv
Denis Davydov [Mon, 11 Jun 2018 05:25:59 +0000 (07:25 +0200)]
Merge pull request #6715 from dsambit/scalapackWrapperTriangularMatInv

Added pXtrtri function to ScaLAPACKMatrix class

6 years agoBlockLinearOperator: Allow identical destination and source
Daniel Arndt [Sun, 10 Jun 2018 15:36:32 +0000 (17:36 +0200)]
BlockLinearOperator: Allow identical destination and source

6 years agoAdd .codecov.yml to .gitattributes 6741/head
Daniel Arndt [Sat, 9 Jun 2018 20:28:59 +0000 (22:28 +0200)]
Add .codecov.yml to .gitattributes

6 years agoMerge pull request #6737 from masterleinad/fix_clang_4_static_constexpr
Matthias Maier [Sat, 9 Jun 2018 19:39:18 +0000 (14:39 -0500)]
Merge pull request #6737 from masterleinad/fix_clang_4_static_constexpr

Move extra static constexpr member declaration to header

6 years agoAdd codecov configuration
Daniel Arndt [Sat, 9 Jun 2018 13:06:46 +0000 (15:06 +0200)]
Add codecov configuration

6 years agoAlternative output for base/utilities_pack_unpack_06 6739/head
Daniel Arndt [Sat, 9 Jun 2018 07:57:24 +0000 (09:57 +0200)]
Alternative output for base/utilities_pack_unpack_06

6 years agoRestrict tests that require DEAL_II_WITH_THREADS=ON 6738/head
Daniel Arndt [Fri, 8 Jun 2018 22:22:41 +0000 (00:22 +0200)]
Restrict tests that require DEAL_II_WITH_THREADS=ON

6 years agoMove extra static constexpr member declaration to header 6737/head
Daniel Arndt [Fri, 8 Jun 2018 20:11:25 +0000 (22:11 +0200)]
Move extra static constexpr member declaration to header

6 years agoMerge pull request #6734 from masterleinad/fix_warning
Daniel Arndt [Fri, 8 Jun 2018 18:21:49 +0000 (20:21 +0200)]
Merge pull request #6734 from masterleinad/fix_warning

Avoid warning reagrding unused Variable in Utilities::unpack

6 years agoMerge pull request #6733 from masterleinad/fix_cuda_exc
Bruno Turcksin [Fri, 8 Jun 2018 17:28:56 +0000 (13:28 -0400)]
Merge pull request #6733 from masterleinad/fix_cuda_exc

Fix compiling with CUDA

6 years agoRetrict directories to apply clang-format to 6736/head
Daniel Arndt [Fri, 8 Jun 2018 16:34:44 +0000 (18:34 +0200)]
Retrict directories to apply clang-format to

6 years agoAvoid warning reagrding unused Variable in Utilities::unpack 6734/head
Daniel Arndt [Fri, 8 Jun 2018 14:59:10 +0000 (16:59 +0200)]
Avoid warning reagrding unused Variable in Utilities::unpack

6 years agoMerge pull request #6731 from masterleinad/silence_tbb_gcc-8_warnings
Daniel Arndt [Fri, 8 Jun 2018 10:28:15 +0000 (12:28 +0200)]
Merge pull request #6731 from masterleinad/silence_tbb_gcc-8_warnings

Silence gcc-8 warnings in bundled TBB

6 years agoFix compiling with CUDA 6733/head
Daniel Arndt [Fri, 8 Jun 2018 10:26:39 +0000 (12:26 +0200)]
Fix compiling with CUDA

6 years agoMerge pull request #6732 from bangerth/module
Matthias Maier [Fri, 8 Jun 2018 05:55:08 +0000 (00:55 -0500)]
Merge pull request #6732 from bangerth/module

Trick doxygen into doing the right thing.

6 years agoMerge pull request #6729 from masterleinad/more_clang_tidy
Wolfgang Bangerth [Fri, 8 Jun 2018 05:43:23 +0000 (23:43 -0600)]
Merge pull request #6729 from masterleinad/more_clang_tidy

More clang-tidy complains

6 years agoTrick doxygen into doing the right thing. 6732/head
Wolfgang Bangerth [Fri, 8 Jun 2018 05:21:18 +0000 (23:21 -0600)]
Trick doxygen into doing the right thing.

Previously, there was a line that started with '4.', which doxygen markdown
interpreted as a entry in a numbered list -- amusingly then starting the
numbering in HTML with '1.'. Avoid this misinterpretation by just reindenting
the whole paragraph.

6 years agoMerge pull request #6730 from masterleinad/const_n_array_elements
Denis Davydov [Fri, 8 Jun 2018 01:59:32 +0000 (03:59 +0200)]
Merge pull request #6730 from masterleinad/const_n_array_elements

Make n_array_elements static const again

6 years agoSilence gcc-8 warnings in bundled TBB 6731/head
Daniel Arndt [Thu, 7 Jun 2018 23:06:38 +0000 (01:06 +0200)]
Silence gcc-8 warnings in bundled TBB

6 years agoMake n_array_elements static const again 6730/head
Daniel Arndt [Thu, 7 Jun 2018 22:38:36 +0000 (00:38 +0200)]
Make n_array_elements static const again

6 years agoMore clang-tidy complains 6729/head
Daniel Arndt [Thu, 7 Jun 2018 15:50:11 +0000 (17:50 +0200)]
More clang-tidy complains

6 years agoMerge pull request #6718 from masterleinad/clang_tidy_5
Daniel Arndt [Thu, 7 Jun 2018 08:25:10 +0000 (10:25 +0200)]
Merge pull request #6718 from masterleinad/clang_tidy_5

Fix clang-tidy findings for Exceptions

6 years agoMerge pull request #6723 from tamiko/license_header
Daniel Arndt [Thu, 7 Jun 2018 08:21:25 +0000 (10:21 +0200)]
Merge pull request #6723 from tamiko/license_header

Update license file in copyright headers

6 years agoMerge pull request #6722 from masterleinad/clang_tidy_4
Daniel Arndt [Thu, 7 Jun 2018 07:47:50 +0000 (09:47 +0200)]
Merge pull request #6722 from masterleinad/clang_tidy_4

Avoid using NOLINT

6 years agoExtend ScaLAPACKMatrix::invert() to use pXtrtri for inversion of triangular matrices. 6715/head
Sambit Das [Thu, 7 Jun 2018 06:59:20 +0000 (02:59 -0400)]
Extend ScaLAPACKMatrix::invert() to use pXtrtri for inversion of triangular matrices.

6 years agoMerge pull request #6601 from marcfehling/quadrant-cell-pairs
Wolfgang Bangerth [Thu, 7 Jun 2018 04:06:03 +0000 (22:06 -0600)]
Merge pull request #6601 from marcfehling/quadrant-cell-pairs

Manage relations of p4est quadrants and dealii cells.

6 years agoManage relations of p4est quadrants and dealii cells. 6601/head
Marc Fehling [Sat, 21 Apr 2018 02:34:41 +0000 (20:34 -0600)]
Manage relations of p4est quadrants and dealii cells.

Use them to rewrite some of the recursively crawling functions.

6 years agoAvoid using NOLINT 6722/head
Daniel Arndt [Wed, 6 Jun 2018 23:36:52 +0000 (01:36 +0200)]
Avoid using NOLINT

6 years agoExplicitly define VectorizedArray::n_array_elements 6718/head
Daniel Arndt [Wed, 6 Jun 2018 22:26:34 +0000 (00:26 +0200)]
Explicitly define VectorizedArray::n_array_elements

6 years agoUpdate license file in copyright header, rest 6723/head
Matthias Maier [Wed, 6 Jun 2018 15:56:30 +0000 (10:56 -0500)]
Update license file in copyright header, rest

6 years agoUpdate license file in copyright header, ./bundled
Matthias Maier [Wed, 6 Jun 2018 15:56:23 +0000 (10:56 -0500)]
Update license file in copyright header, ./bundled

6 years agoUpdate license file in copyright header, ./contrib
Matthias Maier [Wed, 6 Jun 2018 15:55:45 +0000 (10:55 -0500)]
Update license file in copyright header, ./contrib

6 years agoUpdate license file in copyright header, ./doc
Matthias Maier [Wed, 6 Jun 2018 15:55:33 +0000 (10:55 -0500)]
Update license file in copyright header, ./doc

6 years agoUpdate license file in copyright header, ./examples
Matthias Maier [Wed, 6 Jun 2018 15:54:51 +0000 (10:54 -0500)]
Update license file in copyright header, ./examples

6 years agoUpdate license file in copyright header ./tests
Matthias Maier [Wed, 6 Jun 2018 15:54:26 +0000 (10:54 -0500)]
Update license file in copyright header ./tests

6 years agoUpdate license file in copyright header ./include
Matthias Maier [Wed, 6 Jun 2018 15:54:11 +0000 (10:54 -0500)]
Update license file in copyright header ./include

6 years agoUpdate license file in copyright header ./source
Matthias Maier [Wed, 6 Jun 2018 15:53:59 +0000 (10:53 -0500)]
Update license file in copyright header ./source

6 years agoUpdate license file in copyright header, ./cmake
Matthias Maier [Wed, 6 Jun 2018 15:53:44 +0000 (10:53 -0500)]
Update license file in copyright header, ./cmake

6 years agoMerge pull request #6688 from kronbichler/find_all_active_cells_around_point
Matthias Maier [Wed, 6 Jun 2018 16:27:49 +0000 (11:27 -0500)]
Merge pull request #6688 from kronbichler/find_all_active_cells_around_point

Find all active cells around point

6 years agoMerge pull request #6664 from tamiko/add_affine_constraints
Matthias Maier [Wed, 6 Jun 2018 15:48:25 +0000 (10:48 -0500)]
Merge pull request #6664 from tamiko/add_affine_constraints

lac: Add AffineConstraints class

6 years agoadd a last news/changes entry 6664/head
Matthias Maier [Thu, 31 May 2018 15:07:27 +0000 (10:07 -0500)]
add a last news/changes entry

6 years agoFix the gla tests for complex PETSc scalar type
Daniel Arndt [Tue, 29 May 2018 09:29:12 +0000 (11:29 +0200)]
Fix the gla tests for complex PETSc scalar type

6 years agodoc: add incompatibilities news item for create_(boundary_;)mass_matrix
Matthias Maier [Sat, 26 May 2018 03:08:49 +0000 (22:08 -0500)]
doc: add incompatibilities news item for create_(boundary_;)mass_matrix

6 years agodoc: add incompatibilities news item for AffineConstraints/ConstraintMatrix
Matthias Maier [Sat, 26 May 2018 03:04:25 +0000 (22:04 -0500)]
doc: add incompatibilities news item for AffineConstraints/ConstraintMatrix

6 years agoWorkaround: Temporarily define ConstraintMatrix in this header
Matthias Maier [Sat, 26 May 2018 06:59:12 +0000 (01:59 -0500)]
Workaround: Temporarily define ConstraintMatrix in this header

6 years agoBugfix: Add explicit constraint_matrix.h includes to example steps
Matthias Maier [Sat, 26 May 2018 05:39:43 +0000 (00:39 -0500)]
Bugfix: Add explicit constraint_matrix.h includes to example steps

Previously they had been included by chance. Due to the refactoring all
of these includes have to be done explicitly (at least for a short
transition period.)

6 years agoTests: Fix the remaining tests using complex scalars
Daniel Arndt [Mon, 28 May 2018 20:00:05 +0000 (15:00 -0500)]
Tests: Fix the remaining tests using complex scalars

6 years agoTests: Fix nearly all the failing PETSc complex tests
Daniel Arndt [Mon, 28 May 2018 16:22:42 +0000 (18:22 +0200)]
Tests: Fix nearly all the failing PETSc complex tests

6 years agoTests: Fix matrix_free/step-37
Matthias Maier [Mon, 28 May 2018 03:51:25 +0000 (22:51 -0500)]
Tests: Fix matrix_free/step-37

6 years agoTests: Do not include "constraint_matrix.templates.h"
Matthias Maier [Mon, 28 May 2018 03:01:59 +0000 (22:01 -0500)]
Tests: Do not include "constraint_matrix.templates.h"


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