]> https://gitweb.dealii.org/ - dealii.git/log
dealii.git
5 years agoFix a number of exceptions in Triangulation::begin/end/last_...(). 7585/head
Wolfgang Bangerth [Thu, 10 Jan 2019 14:01:48 +0000 (07:01 -0700)]
Fix a number of exceptions in Triangulation::begin/end/last_...().

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 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()

5 years agoImprove the documentation
Daniel Garcia-Sanchez [Wed, 3 Oct 2018 15:52:24 +0000 (17:52 +0200)]
Improve the documentation

Modify copyright years

Remove clang on/off

Use backticks for the types

5 years agoAdd endline
Daniel Garcia-Sanchez [Wed, 3 Oct 2018 15:49:52 +0000 (17:49 +0200)]
Add endline

5 years agoAdd Asserts
Daniel Garcia-Sanchez [Mon, 1 Oct 2018 14:44:47 +0000 (16:44 +0200)]
Add Asserts

5 years agoRemove the warnings of unused variables
Daniel Garcia-Sanchez [Mon, 27 Aug 2018 12:36:39 +0000 (14:36 +0200)]
Remove the warnings of unused variables

There are many warnings of unused variables in release mode because of Assert. Example:

herr_t ret;
ret = H5Pclose(plist);
Assert(ret >= 0, ExcMessage("Error at H5Pclose"));

In order to remove these warnings the declaration of variable ret has been moved from the functions to the class definition of HDF5Object.

5 years agoFormat code
Daniel Garcia-Sanchez [Sun, 26 Aug 2018 15:25:50 +0000 (17:25 +0200)]
Format code

5 years agoRemove irrelevant curly brackets
Daniel Garcia-Sanchez [Sun, 26 Aug 2018 15:24:59 +0000 (17:24 +0200)]
Remove irrelevant curly brackets

5 years agoWrite serial tests for the HDF5 datasets
Daniel Garcia-Sanchez [Sun, 26 Aug 2018 14:43:16 +0000 (16:43 +0200)]
Write serial tests for the HDF5 datasets

5 years agoUse generic container for write_dataset
Daniel Garcia-Sanchez [Sun, 26 Aug 2018 14:07:28 +0000 (16:07 +0200)]
Use generic container for write_dataset

5 years agoAdd support for Vector
Daniel Garcia-Sanchez [Wed, 22 Aug 2018 15:23:32 +0000 (17:23 +0200)]
Add support for Vector

5 years agoPlace most of the instantiations in hdf5.inst.in
Daniel Garcia-Sanchez [Wed, 22 Aug 2018 12:41:28 +0000 (14:41 +0200)]
Place most of the instantiations in hdf5.inst.in

5 years agoWrite parallel tests for the HDF5 datasets
Daniel Garcia-Sanchez [Wed, 22 Aug 2018 09:22:38 +0000 (11:22 +0200)]
Write parallel tests for the HDF5 datasets

5 years agoAdd examples
Daniel Garcia-Sanchez [Wed, 22 Aug 2018 06:29:52 +0000 (08:29 +0200)]
Add examples

5 years agoUse hex values instead of enum values
Daniel Garcia-Sanchez [Tue, 21 Aug 2018 13:55:11 +0000 (15:55 +0200)]
Use hex values instead of enum values

Hex codes are used because the HDF5 Group can deprecate some of the enum codes. For example H5D_MPIO_FILTERS is not defined in 1.10.2 because it is possible to use compressed datasets with the MPI/IO driver.

5 years agoRemove long double and std::complex<long double> instantiations
Daniel Garcia-Sanchez [Mon, 20 Aug 2018 22:06:20 +0000 (00:06 +0200)]
Remove long double and std::complex<long double> instantiations

The std::complex<long double> instantiation creates errors with valgrind.

Although long double does not create errors with valgrind, it is not a widely used.

5 years agoFix doxygen documentation
Daniel Garcia-Sanchez [Sun, 19 Aug 2018 22:08:50 +0000 (00:08 +0200)]
Fix doxygen documentation

5 years agoReplace the template argument T by number
Daniel Garcia-Sanchez [Sun, 19 Aug 2018 21:39:18 +0000 (23:39 +0200)]
Replace the template argument T by number

5 years agoAdd functions read_*()
Daniel Garcia-Sanchez [Sun, 19 Aug 2018 19:16:44 +0000 (21:16 +0200)]
Add functions read_*()

Add read_selection()

Add read_hyperslab()

Add read_none()

5 years agoRemove the quotes in the documentation
Daniel Garcia-Sanchez [Sun, 19 Aug 2018 15:06:48 +0000 (17:06 +0200)]
Remove the quotes in the documentation

5 years agoImprove write_hyperslab()
Daniel Garcia-Sanchez [Sun, 19 Aug 2018 11:53:26 +0000 (13:53 +0200)]
Improve write_hyperslab()

5 years agoRename read_data() to read() and write_data() to write()
Daniel Garcia-Sanchez [Sat, 18 Aug 2018 18:30:51 +0000 (20:30 +0200)]
Rename read_data() to read() and write_data() to write()

5 years agoUse generic Container for write_data and write_data_hyperslab
Daniel Garcia-Sanchez [Sat, 18 Aug 2018 13:28:04 +0000 (15:28 +0200)]
Use generic Container for write_data and write_data_hyperslab

5 years agoGet the pointer to the raw data of FullMatrix
Daniel Garcia-Sanchez [Tue, 14 Aug 2018 22:12:26 +0000 (00:12 +0200)]
Get the pointer to the raw data of FullMatrix

5 years agoAdd functions
Daniel Garcia-Sanchez [Mon, 13 Aug 2018 16:34:04 +0000 (18:34 +0200)]
Add functions

Add read_data() function

Add io_mode() and check_io_mode() functions

Add local_no_collective_cause() and global_no_collective_cause()

5 years agoWrite tests for HDF5 attributes
Daniel Garcia-Sanchez [Tue, 7 Aug 2018 20:54:30 +0000 (22:54 +0200)]
Write tests for HDF5 attributes

5 years agoConstructor for opening a dataset
Daniel Garcia-Sanchez [Tue, 7 Aug 2018 20:06:37 +0000 (22:06 +0200)]
Constructor for opening a dataset

5 years agoWrite UTF8 string attributes
Daniel Garcia-Sanchez [Mon, 6 Aug 2018 21:34:18 +0000 (23:34 +0200)]
Write UTF8 string attributes

5 years agoUse templates for the function members of DataSet
Daniel Garcia-Sanchez [Sun, 5 Aug 2018 15:24:33 +0000 (17:24 +0200)]
Use templates for the function members of DataSet

5 years agoCheck support for HDF5 and MPI
Daniel Garcia-Sanchez [Fri, 3 Aug 2018 09:22:47 +0000 (11:22 +0200)]
Check support for HDF5 and MPI

5 years agoAdd support for all the scalar and complex types
Daniel Garcia-Sanchez [Thu, 2 Aug 2018 18:16:56 +0000 (20:16 +0200)]
Add support for all the scalar and complex types

Add FullMatrix support in write_dataset

Modify the namespace

Place get_hdf5_datatype in the internal namespace

5 years agoAdd HDF5 classes
Daniel Garcia-Sanchez [Thu, 2 Aug 2018 11:09:54 +0000 (13:09 +0200)]
Add HDF5 classes

5 years agoAdded tests and support for non-mpi to GridTools::build_global_tree 7569/head
Giovanni Alzetta [Mon, 7 Jan 2019 11:09:28 +0000 (12:09 +0100)]
Added tests and support for non-mpi to GridTools::build_global_tree

5 years agoImproved NonMatching::create_coupling_matrix algorithm 7564/head
Giovanni Alzetta [Sun, 6 Jan 2019 17:11:07 +0000 (18:11 +0100)]
Improved NonMatching::create_coupling_matrix algorithm

5 years agoMerge pull request #7474 from starki0815/dealii_extract_boundary_mesh_patched
Wolfgang Bangerth [Wed, 9 Jan 2019 08:50:45 +0000 (01:50 -0700)]
Merge pull request #7474 from starki0815/dealii_extract_boundary_mesh_patched

Fix bugs in extract_boundary_mesh

5 years agoMerge pull request #7574 from masterleinad/test_fallthrough
Matthias Maier [Wed, 9 Jan 2019 02:02:10 +0000 (20:02 -0600)]
Merge pull request #7574 from masterleinad/test_fallthrough

Check [[fallthrough]] instead of assuming it when C++17 support is enabled

5 years agoMerge pull request #7570 from masterleinad/loop-convert_1
Daniel Arndt [Wed, 9 Jan 2019 01:15:27 +0000 (02:15 +0100)]
Merge pull request #7570 from masterleinad/loop-convert_1

Use range-based for loops in examples and expand_instantiations

5 years agoMerge pull request #7573 from masterleinad/require_openmp_cuda
Bruno Turcksin [Wed, 9 Jan 2019 00:44:08 +0000 (19:44 -0500)]
Merge pull request #7573 from masterleinad/require_openmp_cuda

Require OpenMP for CUDA support

5 years agoOptimizing NonMatching::create_coupling_sparsity_pattern use of compute point locations 7563/head
Giovanni Alzetta [Sat, 5 Jan 2019 23:03:01 +0000 (00:03 +0100)]
Optimizing NonMatching::create_coupling_sparsity_pattern use of compute point locations

5 years agoCheck [[fallthrough]] instead of assuming it when C++17 support is enabled 7574/head
Daniel Arndt [Tue, 8 Jan 2019 20:25:26 +0000 (21:25 +0100)]
Check [[fallthrough]] instead of assuming it when C++17 support is enabled

5 years agoRequire OpenMP for CUDA support 7573/head
Daniel Arndt [Tue, 8 Jan 2019 20:28:47 +0000 (21:28 +0100)]
Require OpenMP for CUDA support

5 years agoUse range-based for loops in examples and expand_instantiations 7570/head
Daniel Arndt [Sat, 5 Jan 2019 20:44:37 +0000 (21:44 +0100)]
Use range-based for loops in examples and expand_instantiations

5 years agoFix failed tests for extract_boundary_mesh and add new test 7474/head
Sebastian Stark [Tue, 18 Dec 2018 12:37:03 +0000 (14:37 +0200)]
Fix failed tests for extract_boundary_mesh and add new test

add codim_one/extract_boundary_mesh_15
  - The test checks whether extract_boundary_mesh produces correct results for 2d and 3d. In particular, it checks whether #7474 succesfully fixes #7467.

fix manifold/polar_manifold_04:
  - failed because of different vertex ordering in 2d and 3d with the new version in order to get consistent outward facing normals
  - contains a bug in itself in that the north and south poles are not properly excluded in 3d (only the origin is excluded in the code)
  -> solution: fix bug in test and update output file
All other failed tests have been fixed by updating the output file

5 years agoFix bugs in extract_boundary_mesh.
Sebastian Stark [Mon, 26 Nov 2018 08:27:18 +0000 (10:27 +0200)]
Fix bugs in extract_boundary_mesh.

In 3d, extract_boundary_mesh swaps vertices to get consistent boundary cell orientations. However, this swapping was so far not taken into account during the assembly of the map between boundary cells and corresponding faces of the volume cells. Fixing the latter required substantial changes (a quick and dirty fix would have been possible in principle, but certainly not clean) to extract_boundary_mesh because the (local) face indices of the volume cells must be known when the map is assembled. Also, the algorithm to do the refinement of the boundary mesh has been modified such that map lookups are no longer necessary. Moreover, vertex swapping has been introduced also for the 2d case in order to make the 2d behavior consistent with the 3d behavior (in previous versions of the function, the normal vector of the boundary mesh pointed always into the domain in 3d, whereas it pointed either into or out of the domain in 2d depending on the situation). Further, the normals have been adjusted to generally face outward.  Fixes #7467.

5 years agoMerge pull request #7440 from masterleinad/restrict_subscribe
Daniel Arndt [Tue, 8 Jan 2019 14:39:04 +0000 (15:39 +0100)]
Merge pull request #7440 from masterleinad/restrict_subscribe

 Disallow using rvalue references for Subscriptor::(un)?subscribe

5 years agoMerge pull request #7571 from masterleinad/replace_size_t
Wolfgang Bangerth [Tue, 8 Jan 2019 13:51:23 +0000 (06:51 -0700)]
Merge pull request #7571 from masterleinad/replace_size_t

Replace size_t by std::size_t

5 years agoDisallow using rvalue references for Subscriptor::(un)?subscribe 7440/head
Daniel Arndt [Mon, 12 Nov 2018 17:25:43 +0000 (18:25 +0100)]
Disallow using rvalue references for Subscriptor::(un)?subscribe


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