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5 years agoDoFTools: restructure set_periodicity_constraints, part III
Matthias Maier [Fri, 18 Jan 2019 21:01:55 +0000 (15:01 -0600)]
DoFTools: restructure set_periodicity_constraints, part III

The last commit in this series fixes up the remainder of the
set_periodicity_constraints function.

5 years agoDoFTools: restructure set_periodicity_constraints, part II
Matthias Maier [Fri, 18 Jan 2019 20:19:11 +0000 (14:19 -0600)]
DoFTools: restructure set_periodicity_constraints, part II

This commit simplifies a code path to identify "identity constraints". In
preparation for support for complex-valued interpolation matrices, the logic
has been slightly generalized to support arbitrary, nonzero scaling parameters.

This commit does not introduce a functional change.

5 years agoDoFTools: restructure set_periodicity_constraints
Matthias Maier [Fri, 18 Jan 2019 17:14:09 +0000 (11:14 -0600)]
DoFTools: restructure set_periodicity_constraints

This commit restructures the function set_periodicity_constraints. Over
the last years (and after fixing about a dozen periodicity related bugs)
this function has gotten out of control. The aim for this restructuring
is to put back some order into the function. This is achieved by:

 - Merging loops and if clauses that were redundant.

 - Minor code cleanup.

 - Switching to a different idiom:

   if(... special case ...)
     {
       // do special case
       continue;
     }

   // next special case

   This saves about 5 (!) levels of indentation and makes the control
   flow significantly more obvious to (a) comment on and (b) understand
   again later.

This commit does not introduce a functional change.

5 years agoMerge pull request #7607 from drwells/vector-operation-constness
Daniel Arndt [Fri, 18 Jan 2019 08:21:22 +0000 (09:21 +0100)]
Merge pull request #7607 from drwells/vector-operation-constness

Mark some more things as const in Vector internals.

5 years agoMark some more things as const in Vector internals. 7607/head
David Wells [Thu, 3 Jan 2019 23:17:48 +0000 (18:17 -0500)]
Mark some more things as const in Vector internals.

5 years agoMerge pull request #7602 from tjhei/fix-clang-tidy-script
Daniel Arndt [Thu, 17 Jan 2019 18:33:11 +0000 (19:33 +0100)]
Merge pull request #7602 from tjhei/fix-clang-tidy-script

fix clang tidy script

5 years agoMerge pull request #7598 from masterleinad/loop-convert_6
David Wells [Wed, 16 Jan 2019 21:07:41 +0000 (16:07 -0500)]
Merge pull request #7598 from masterleinad/loop-convert_6

Use ranged-base for loop in numerics and multigrid

5 years agoMerge pull request #7593 from drwells/remove-vector-view
Daniel Arndt [Tue, 15 Jan 2019 22:37:11 +0000 (23:37 +0100)]
Merge pull request #7593 from drwells/remove-vector-view

Remove VectorView.

5 years agoMerge pull request #7591 from marcfehling/fix-pre-distributed-refinement
Daniel Arndt [Tue, 15 Jan 2019 20:55:03 +0000 (21:55 +0100)]
Merge pull request #7591 from marcfehling/fix-pre-distributed-refinement

Changed point at which p::d::Tria::pre_distributed_refinement is triggered.

5 years agoremove muparser setting 7602/head
Timo Heister [Tue, 15 Jan 2019 19:32:37 +0000 (12:32 -0700)]
remove muparser setting

5 years agodo not allow bundled
Timo Heister [Tue, 15 Jan 2019 16:20:20 +0000 (09:20 -0700)]
do not allow bundled

5 years agofix clang tidy script
Timo Heister [Tue, 15 Jan 2019 16:17:49 +0000 (09:17 -0700)]
fix clang tidy script

- fix additional args ($@)
- do not quote ARGS, otherwise it doesn't work

5 years agoChanged point at which p::d::Tria::pre_distributed_refinement is triggered. 7591/head
Marc Fehling [Fri, 11 Jan 2019 17:14:45 +0000 (18:14 +0100)]
Changed point at which p::d::Tria::pre_distributed_refinement is triggered.

5 years agoMerge pull request #7601 from masterleinad/use_modenize_use_nullptr
David Wells [Tue, 15 Jan 2019 02:48:34 +0000 (21:48 -0500)]
Merge pull request #7601 from masterleinad/use_modenize_use_nullptr

Use modernize-use-nullptr

5 years agoUse ranged-based for loop in include/multigrid 7598/head
Daniel Arndt [Sun, 6 Jan 2019 16:04:14 +0000 (17:04 +0100)]
Use ranged-based for loop in include/multigrid

5 years agoUse ranged-based for loop in source/multigrid
Daniel Arndt [Wed, 9 Jan 2019 09:19:43 +0000 (10:19 +0100)]
Use ranged-based for loop in source/multigrid

5 years agoUse ranged-based for loop in include/numerics
Daniel Arndt [Sun, 6 Jan 2019 16:32:05 +0000 (17:32 +0100)]
Use ranged-based for loop in include/numerics

5 years agoUse ranged-based for loop in source/numerics
Daniel Arndt [Wed, 9 Jan 2019 09:20:19 +0000 (10:20 +0100)]
Use ranged-based for loop in source/numerics

5 years agoUse modernize-use-nullptr 7601/head
Daniel Arndt [Mon, 14 Jan 2019 14:57:02 +0000 (15:57 +0100)]
Use modernize-use-nullptr

5 years agoMerge pull request #7600 from drwells/remove-extra-semicolons
Daniel Arndt [Mon, 14 Jan 2019 13:07:00 +0000 (14:07 +0100)]
Merge pull request #7600 from drwells/remove-extra-semicolons

Remove unnecessary semicolons from source files.

5 years agoRemove unnecessary semicolons from source files. 7600/head
David Wells [Sun, 13 Jan 2019 23:17:02 +0000 (18:17 -0500)]
Remove unnecessary semicolons from source files.

5 years agoMerge pull request #7599 from Rombur/misc
Daniel Arndt [Sun, 13 Jan 2019 15:04:05 +0000 (16:04 +0100)]
Merge pull request #7599 from Rombur/misc

CUDA instantiation

5 years agoRemove unused code 7599/head
Bruno Turcksin [Sun, 13 Jan 2019 03:02:29 +0000 (22:02 -0500)]
Remove unused code

5 years agoAdd missing instantiations for ditributed CUDA vectors
Bruno Turcksin [Sun, 13 Jan 2019 03:02:13 +0000 (22:02 -0500)]
Add missing instantiations for ditributed CUDA vectors

5 years agoMerge pull request #7595 from masterleinad/loop-convert_5
David Wells [Sat, 12 Jan 2019 18:07:08 +0000 (13:07 -0500)]
Merge pull request #7595 from masterleinad/loop-convert_5

Use range-based loops in dofs and distributed

5 years agoMerge pull request #7596 from masterleinad/delete_fevalues_copy_constructor
David Wells [Sat, 12 Jan 2019 18:06:51 +0000 (13:06 -0500)]
Merge pull request #7596 from masterleinad/delete_fevalues_copy_constructor

Actually delete copy constructors for FEValues*

5 years agoActually delete copy constructors for FEValues* 7596/head
Daniel Arndt [Sat, 12 Jan 2019 14:15:25 +0000 (15:15 +0100)]
Actually delete copy constructors for FEValues*

5 years agoUse range-based for loop in source/distributed 7595/head
Daniel Arndt [Sun, 6 Jan 2019 18:54:44 +0000 (19:54 +0100)]
Use range-based for loop in source/distributed

5 years agoUse range-based for loop in source/dofs
Daniel Arndt [Sun, 6 Jan 2019 19:18:32 +0000 (20:18 +0100)]
Use range-based for loop in source/dofs

5 years agoMerge pull request #7594 from drwells/use-emplace-over-dtor
Daniel Arndt [Sat, 12 Jan 2019 09:55:57 +0000 (10:55 +0100)]
Merge pull request #7594 from drwells/use-emplace-over-dtor

Use emplace_back over an in-place destructor/new.

5 years agoRemove VectorView. 7593/head
David Wells [Thu, 3 Jan 2019 21:58:11 +0000 (16:58 -0500)]
Remove VectorView.

This class was deprecated before the 9.0 release.

5 years agoUse emplace_back over an in-place destructor/new. 7594/head
David Wells [Sat, 12 Jan 2019 01:24:28 +0000 (20:24 -0500)]
Use emplace_back over an in-place destructor/new.

5 years agoMerge pull request #7590 from masterleinad/loop-convert_4
David Wells [Sat, 12 Jan 2019 01:04:30 +0000 (20:04 -0500)]
Merge pull request #7590 from masterleinad/loop-convert_4

Use range-based for loops in grid files

5 years agoUse std::sets in GridOut::write_svg 7590/head
Daniel Arndt [Fri, 11 Jan 2019 17:01:15 +0000 (18:01 +0100)]
Use std::sets in GridOut::write_svg

5 years agoUse range-based for loops in include/grid
Daniel Arndt [Mon, 7 Jan 2019 10:57:39 +0000 (11:57 +0100)]
Use range-based for loops in include/grid

5 years agoUse range-based for loops in source/grid
Daniel Arndt [Wed, 9 Jan 2019 08:51:21 +0000 (09:51 +0100)]
Use range-based for loops in source/grid

5 years agoMerge pull request #7586 from masterleinad/loop-convert_3
Daniel Arndt [Fri, 11 Jan 2019 08:50:57 +0000 (09:50 +0100)]
Merge pull request #7586 from masterleinad/loop-convert_3

Use ranged-based for loops in hp

5 years agoMerge pull request #7572 from marcfehling/fix-fourier
Daniel Arndt [Thu, 10 Jan 2019 22:28:30 +0000 (23:28 +0100)]
Merge pull request #7572 from marcfehling/fix-fourier

Fixed indices in FESeries::Fourier::set_k_vectors().

5 years agoMerge pull request #7580 from masterleinad/more_fallthrough
Daniel Arndt [Thu, 10 Jan 2019 20:38:09 +0000 (21:38 +0100)]
Merge pull request #7580 from masterleinad/more_fallthrough

Use more flags in [[fallthrough]] checks

5 years agoUse range-based for loops in include/hp 7586/head
Daniel Arndt [Mon, 7 Jan 2019 11:00:04 +0000 (12:00 +0100)]
Use range-based for loops in include/hp

5 years agoUse range-based for loops in source/hp
Daniel Arndt [Sun, 6 Jan 2019 22:45:15 +0000 (23:45 +0100)]
Use range-based for loops in source/hp

5 years agoMerge pull request #7575 from masterleinad/loop-convert_2
Matthias Maier [Thu, 10 Jan 2019 17:38:35 +0000 (11:38 -0600)]
Merge pull request #7575 from masterleinad/loop-convert_2

Use range-based for loops II

5 years agoMerge pull request #7582 from bangerth/exception
Daniel Arndt [Thu, 10 Jan 2019 17:03:47 +0000 (18:03 +0100)]
Merge pull request #7582 from bangerth/exception

Remove a pointless assertion.

5 years agoRemove a pointless exception. 7582/head
Wolfgang Bangerth [Thu, 10 Jan 2019 13:52:22 +0000 (06:52 -0700)]
Remove a pointless exception.

5 years agoMerge pull request #7564 from GivAlz/CouplingMatrix
Daniel Arndt [Thu, 10 Jan 2019 10:44:24 +0000 (11:44 +0100)]
Merge pull request #7564 from GivAlz/CouplingMatrix

Optimizing NonMatching::create_coupling_mass_matrix

5 years agoMerge pull request #7563 from GivAlz/CouplingSparsity
Daniel Arndt [Thu, 10 Jan 2019 10:43:01 +0000 (11:43 +0100)]
Merge pull request #7563 from GivAlz/CouplingSparsity

Optimizing NonMatching::create_coupling_sparsity_pattern

5 years agoUse more flags in [[fallthrough]] checks 7580/head
Daniel Arndt [Thu, 10 Jan 2019 09:24:48 +0000 (10:24 +0100)]
Use more flags in [[fallthrough]] checks

5 years agoUse range-based for loops in source/non_matching 7575/head
Daniel Arndt [Wed, 9 Jan 2019 10:07:20 +0000 (11:07 +0100)]
Use range-based for loops in source/non_matching

5 years agoUse range-based for loops in source/opencascade
Daniel Arndt [Mon, 7 Jan 2019 01:09:38 +0000 (02:09 +0100)]
Use range-based for loops in source/opencascade

5 years agoUse range-based for loops in source/particles
Daniel Arndt [Mon, 7 Jan 2019 01:10:06 +0000 (02:10 +0100)]
Use range-based for loops in source/particles

5 years agoMerge pull request #7020 from dangars/hdf5
Daniel Arndt [Wed, 9 Jan 2019 20:57:54 +0000 (21:57 +0100)]
Merge pull request #7020 from dangars/hdf5

Add HDF5 classes

5 years agoMerge pull request #7567 from bangerth/doc-update
David Wells [Wed, 9 Jan 2019 20:48:07 +0000 (15:48 -0500)]
Merge pull request #7567 from bangerth/doc-update

Update some documentation.

5 years agoChangelog entry 7020/head
Daniel Garcia-Sanchez [Wed, 9 Jan 2019 18:38:53 +0000 (19:38 +0100)]
Changelog entry

5 years agoImprove the documentation
Daniel Garcia-Sanchez [Thu, 29 Nov 2018 16:35:32 +0000 (17:35 +0100)]
Improve the documentation

5 years agoReorder functions get/set_query_io_mode()
Daniel Garcia-Sanchez [Thu, 29 Nov 2018 15:58:00 +0000 (16:58 +0100)]
Reorder functions get/set_query_io_mode()

5 years agoAdd functions set_plist() and release_plist()
Daniel Garcia-Sanchez [Wed, 28 Nov 2018 19:00:41 +0000 (20:00 +0100)]
Add functions set_plist() and release_plist()

5 years agoRemove std::vector copy
Daniel Garcia-Sanchez [Tue, 27 Nov 2018 13:39:08 +0000 (14:39 +0100)]
Remove std::vector copy

5 years agoUse const reference instead of rvalue
Daniel Garcia-Sanchez [Mon, 26 Nov 2018 16:03:14 +0000 (17:03 +0100)]
Use const reference instead of rvalue

5 years agoCreate a list with a more clear syntax
Daniel Garcia-Sanchez [Fri, 23 Nov 2018 16:27:19 +0000 (17:27 +0100)]
Create a list with a more clear syntax

5 years agoSpecify the argument in the lambda funcions
Daniel Garcia-Sanchez [Thu, 22 Nov 2018 17:50:16 +0000 (18:50 +0100)]
Specify the argument in the lambda funcions

Generic lambdas is a C++14 feature

5 years agoMake the arguments const
Daniel Garcia-Sanchez [Thu, 22 Nov 2018 17:39:07 +0000 (18:39 +0100)]
Make the arguments const

5 years agoAdd get_name()
Daniel Garcia-Sanchez [Wed, 21 Nov 2018 19:40:25 +0000 (20:40 +0100)]
Add get_name()

5 years agoMake const the functions open_* and create_*
Daniel Garcia-Sanchez [Thu, 15 Nov 2018 15:40:55 +0000 (16:40 +0100)]
Make const the functions open_* and create_*

5 years agoUse make_array_view(container_object).data()
Daniel Garcia-Sanchez [Thu, 15 Nov 2018 14:52:25 +0000 (15:52 +0100)]
Use make_array_view(container_object).data()

Obtain a pointer to the container raw data using make_array_view(container_object).data(). Remove the functions get_container_pointer().

5 years agoImprove the documentation
Daniel Garcia-Sanchez [Fri, 2 Nov 2018 17:09:06 +0000 (18:09 +0100)]
Improve the documentation

5 years agoRename group() to open_group()
Daniel Garcia-Sanchez [Fri, 2 Nov 2018 12:30:39 +0000 (13:30 +0100)]
Rename group() to open_group()

5 years agoMake get_attribute const
Daniel Garcia-Sanchez [Wed, 31 Oct 2018 16:16:17 +0000 (17:16 +0100)]
Make get_attribute const

5 years agoReorder parameters
Daniel Garcia-Sanchez [Wed, 31 Oct 2018 15:57:44 +0000 (16:57 +0100)]
Reorder parameters

5 years agoAdd test hdf5_06
Daniel Garcia-Sanchez [Tue, 30 Oct 2018 16:52:26 +0000 (17:52 +0100)]
Add test hdf5_06

The test hdf5_06 is the serial version of hdf5_05

5 years agoAdd test for Vector and write/read selection
Daniel Garcia-Sanchez [Tue, 30 Oct 2018 10:02:40 +0000 (11:02 +0100)]
Add test for Vector and write/read selection

5 years agoUse Container in read_selection and write_selection
Daniel Garcia-Sanchez [Tue, 30 Oct 2018 09:26:35 +0000 (10:26 +0100)]
Use Container in read_selection and write_selection

5 years agoUse overload instead of enable_if
Daniel Garcia-Sanchez [Tue, 30 Oct 2018 07:36:45 +0000 (08:36 +0100)]
Use overload instead of enable_if

5 years agoMake herr_t ret local variable
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 21:40:13 +0000 (22:40 +0100)]
Make herr_t ret local variable

5 years agoRename enum Mode
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 21:18:27 +0000 (22:18 +0100)]
Rename enum Mode

5 years agoImprove the documentation
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 20:44:04 +0000 (21:44 +0100)]
Improve the documentation

Modify the location of clang off

Add in the documentation the MPI requirements

Fix typos

5 years agoRename dataset() to open_dataset()
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 20:37:19 +0000 (21:37 +0100)]
Rename dataset() to open_dataset()

5 years agoAdd complex=off for the test hdf5_05
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 19:53:10 +0000 (20:53 +0100)]
Add complex=off for the test hdf5_05

5 years agoAdd hdf5_05.mpirun=1.output
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 19:42:37 +0000 (20:42 +0100)]
Add hdf5_05.mpirun=1.output

5 years agoAdd tests in tests/base/hdf5_05.cc
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 19:26:38 +0000 (20:26 +0100)]
Add tests in tests/base/hdf5_05.cc

5 years agoAdd read_hyperslab()
Daniel Garcia-Sanchez [Mon, 29 Oct 2018 19:19:26 +0000 (20:19 +0100)]
Add read_hyperslab()

5 years agoSqueeze the dimensions of FullMatrix in initialize_container()
Daniel Garcia-Sanchez [Sat, 20 Oct 2018 12:26:59 +0000 (14:26 +0200)]
Squeeze the dimensions of FullMatrix in initialize_container()

5 years agoAdd test hdf5_05
Daniel Garcia-Sanchez [Tue, 16 Oct 2018 10:16:38 +0000 (12:16 +0200)]
Add test hdf5_05

The test hdf5_05 is based on the test hdf5_03

5 years agoHDF5 tests with_complex_values=off
Daniel Garcia-Sanchez [Mon, 15 Oct 2018 21:09:12 +0000 (23:09 +0200)]
HDF5 tests with_complex_values=off

5 years agoAdd the option "with_complex_values=on" in the output files of the tests
Daniel Garcia-Sanchez [Mon, 15 Oct 2018 13:20:30 +0000 (15:20 +0200)]
Add the option "with_complex_values=on" in the output files of the tests

5 years agoDeclare variables as const
Daniel Garcia-Sanchez [Tue, 9 Oct 2018 19:27:35 +0000 (21:27 +0200)]
Declare variables as const

5 years agoImprove the documentation
Daniel Garcia-Sanchez [Tue, 9 Oct 2018 14:37:55 +0000 (16:37 +0200)]
Improve the documentation

Thread safety documentation

Modify the hyperslab documentation

5 years agoUse two functions instead of a template
Daniel Garcia-Sanchez [Tue, 9 Oct 2018 14:18:58 +0000 (16:18 +0200)]
Use two functions instead of a template

Instead of a templated get_io_mode() function. Two functions have been defined:
- std::string get_io_mode();
- H5D_mpio_actual_io_mode_t get_io_mode_as_hdf5_type();

And the same for get_local_no_collective_cause() and get_global_no_collective_cause()

5 years agoRename functions
Daniel Garcia-Sanchez [Mon, 8 Oct 2018 13:22:35 +0000 (15:22 +0200)]
Rename functions

5 years agoSeparate functions by three empty lines
Daniel Garcia-Sanchez [Mon, 8 Oct 2018 09:27:07 +0000 (11:27 +0200)]
Separate functions by three empty lines

5 years agoUse make_shared in get_hdf5_datatype()
Daniel Garcia-Sanchez [Sun, 7 Oct 2018 11:29:35 +0000 (13:29 +0200)]
Use make_shared in get_hdf5_datatype()

5 years agoDocument the constructors of Group and File
Daniel Garcia-Sanchez [Sat, 6 Oct 2018 11:12:35 +0000 (13:12 +0200)]
Document the constructors of Group and File

5 years agoUse lambda function in no_collective_cause_to_string()
Daniel Garcia-Sanchez [Fri, 5 Oct 2018 21:05:01 +0000 (23:05 +0200)]
Use lambda function in no_collective_cause_to_string()

5 years agoImprove the documentation
Daniel Garcia-Sanchez [Fri, 5 Oct 2018 16:47:18 +0000 (18:47 +0200)]
Improve the documentation

Document helper functions

Document valid Containers

Document read_selection() and write_selection()

Use @p for arguments in the documentation

Document initialize_container

Fix typo

Documentation of the rank of HDF5 datasets and hyperslabs

5 years agoReplace template template Containers by template Containers
Daniel Garcia-Sanchez [Fri, 5 Oct 2018 15:54:46 +0000 (17:54 +0200)]
Replace template template Containers by template Containers

5 years agoMerge pull request #7569 from GivAlz/AddTestGlobalTree
Daniel Arndt [Wed, 9 Jan 2019 18:18:47 +0000 (19:18 +0100)]
Merge pull request #7569 from GivAlz/AddTestGlobalTree

Add test and support for non-mpi to GridTools::build_global_tree

5 years agoImprove the documentation
Daniel Garcia-Sanchez [Fri, 5 Oct 2018 09:56:43 +0000 (11:56 +0200)]
Improve the documentation

Improve the documentation of hyperslab

Document hdf5_reference std::shared_ptr<>

Document DataSet constructors

5 years agoPass parameters by reference
Daniel Garcia-Sanchez [Thu, 4 Oct 2018 17:16:26 +0000 (19:16 +0200)]
Pass parameters by reference

5 years agoMove enum Mode
Daniel Garcia-Sanchez [Thu, 4 Oct 2018 15:59:41 +0000 (17:59 +0200)]
Move enum Mode

5 years agoDefine mpi variable as const
Daniel Garcia-Sanchez [Thu, 4 Oct 2018 15:04:17 +0000 (17:04 +0200)]
Define mpi variable as const

5 years agoRename check_io_mode() to query_io_mode()
Daniel Garcia-Sanchez [Thu, 4 Oct 2018 09:41:03 +0000 (11:41 +0200)]
Rename check_io_mode() to query_io_mode()


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