]> https://gitweb.dealii.org/ - dealii.git/log
dealii.git
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 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 agoMerge pull request #7568 from bangerth/cleanups
Daniel Arndt [Tue, 8 Jan 2019 09:39:37 +0000 (10:39 +0100)]
Merge pull request #7568 from bangerth/cleanups

Some minor cleanups in GridTools.

5 years agoSome cleanups in GridTools. 7568/head
Wolfgang Bangerth [Mon, 7 Jan 2019 20:07:06 +0000 (13:07 -0700)]
Some cleanups in GridTools.

5 years agoMerge pull request #7565 from bangerth/fix-test
Daniel Arndt [Mon, 7 Jan 2019 17:49:25 +0000 (18:49 +0100)]
Merge pull request #7565 from bangerth/fix-test

Use correct data type for a random number.

5 years agoUse correct data type for a random number. 7565/head
Wolfgang Bangerth [Mon, 7 Jan 2019 14:04:50 +0000 (07:04 -0700)]
Use correct data type for a random number.

5 years agoMerge pull request #7303 from masterleinad/cuda_aware_mpi
Martin Kronbichler [Mon, 7 Jan 2019 09:37:43 +0000 (10:37 +0100)]
Merge pull request #7303 from masterleinad/cuda_aware_mpi

Allow using CUDA-aware MPI

5 years agoMerge pull request #7001 from GivAlz/GlobalTree
Luca Heltai [Mon, 7 Jan 2019 08:24:29 +0000 (09:24 +0100)]
Merge pull request #7001 from GivAlz/GlobalTree

Adding global tree of bounding boxes

5 years agoAdding global tree of bounding boxes 7001/head
Giovanni Alzetta [Mon, 30 Jul 2018 11:51:11 +0000 (13:51 +0200)]
Adding global tree of bounding boxes

5 years agoMerge pull request #7562 from masterleinad/fix_nvcc_warnings
Bruno Turcksin [Fri, 4 Jan 2019 22:04:05 +0000 (17:04 -0500)]
Merge pull request #7562 from masterleinad/fix_nvcc_warnings

Fix nvcc warnings

5 years agoFix nvcc warnings 7562/head
Daniel Arndt [Fri, 4 Jan 2019 21:34:02 +0000 (22:34 +0100)]
Fix nvcc warnings

5 years agoChangelog entry 7303/head
Daniel Arndt [Fri, 4 Jan 2019 15:44:13 +0000 (16:44 +0100)]
Changelog entry

5 years agoMake gather kernel more general
Bruno Turcksin [Tue, 18 Dec 2018 14:14:09 +0000 (14:14 +0000)]
Make gather kernel more general

This make the index type a template parameter so that gather
can be used export_to_ghosted_array_start when using 64 bit indices.

5 years agoOptimization of export_to_ghosted_array_start()
Bruno Turcksin [Mon, 26 Nov 2018 13:51:38 +0000 (13:51 +0000)]
Optimization of export_to_ghosted_array_start()

When use CUDA-aware MPI, the sets of local indices that are ghost on other
processors are expanded in arrays. This allows for a sharp reduction in the
number of kernel launches in export_to_ghosted_array_start().

5 years agoAdd gather cuda kernel
Bruno Turcksin [Mon, 26 Nov 2018 13:48:58 +0000 (13:48 +0000)]
Add gather cuda kernel

5 years agoLet ArrayView have a MemorySpace template parameter
Daniel Arndt [Fri, 2 Nov 2018 19:33:25 +0000 (20:33 +0100)]
Let ArrayView have a MemorySpace template parameter

5 years agoUpdate Partitioner::(import|export)_to_ghosted_array_(start|finish)
Daniel Arndt [Thu, 1 Nov 2018 11:54:29 +0000 (12:54 +0100)]
Update Partitioner::(import|export)_to_ghosted_array_(start|finish)

5 years agoUse CUDA-aware MPI in Vector::compress*
Daniel Arndt [Wed, 31 Oct 2018 18:42:46 +0000 (19:42 +0100)]
Use CUDA-aware MPI in Vector::compress*

5 years agoChange position of template argument in CUDAWrappers::kernel
Daniel Arndt [Wed, 31 Oct 2018 18:41:09 +0000 (19:41 +0100)]
Change position of template argument in CUDAWrappers::kernel

5 years agoLet Partitioner have a MemorySpace template parameter
Daniel Arndt [Wed, 31 Oct 2018 18:38:05 +0000 (19:38 +0100)]
Let Partitioner have a MemorySpace template parameter

5 years agoUse MemorySpace for import_data
Daniel Arndt [Thu, 18 Oct 2018 20:21:57 +0000 (22:21 +0200)]
Use MemorySpace for import_data

5 years ago Introduce a configuration variable DEAL_II_WITH_CUDA_AWARE_MPI
Daniel Arndt [Thu, 18 Oct 2018 20:07:17 +0000 (22:07 +0200)]
 Introduce a configuration variable DEAL_II_WITH_CUDA_AWARE_MPI

5 years agoMerge pull request #7558 from masterleinad/restrict_test
Wolfgang Bangerth [Wed, 2 Jan 2019 15:20:01 +0000 (08:20 -0700)]
Merge pull request #7558 from masterleinad/restrict_test

Restrict vector_tools/interpolate_with_material_id_02

5 years agoMerge pull request #7555 from masterleinad/fix_distributed_compute_point_locations_02
Wolfgang Bangerth [Wed, 2 Jan 2019 15:19:47 +0000 (08:19 -0700)]
Merge pull request #7555 from masterleinad/fix_distributed_compute_point_locations_02

Fix distributed_compute_point_locations_02

5 years agoMerge pull request #7561 from bangerth/cleanup
Daniel Arndt [Wed, 2 Jan 2019 08:03:50 +0000 (09:03 +0100)]
Merge pull request #7561 from bangerth/cleanup

Clean up some functions in FEFieldFunction.

5 years agoMerge pull request #7560 from drwells/trilinos-c-casts
David Wells [Tue, 1 Jan 2019 16:47:11 +0000 (11:47 -0500)]
Merge pull request #7560 from drwells/trilinos-c-casts

Clean up Trilinos casts.

5 years agoClean up some functions in FEFieldFunction. 7561/head
Wolfgang Bangerth [Mon, 31 Dec 2018 16:28:30 +0000 (09:28 -0700)]
Clean up some functions in FEFieldFunction.

5 years agoMerge pull request #7559 from davydden/feature/apply_givens_rotation
Wolfgang Bangerth [Sun, 30 Dec 2018 18:37:56 +0000 (11:37 -0700)]
Merge pull request #7559 from davydden/feature/apply_givens_rotation

add functions to apply Givens rotation

5 years agoadd functions to apply Givens rotation 7559/head
Denis Davydov [Fri, 21 Sep 2018 10:49:43 +0000 (12:49 +0200)]
add functions to apply Givens rotation

5 years agoClean up some casts in the Trilinos wrappers. 7560/head
David Wells [Sun, 30 Dec 2018 15:38:51 +0000 (10:38 -0500)]
Clean up some casts in the Trilinos wrappers.

Many of the const_casts and integral downcasts are not necessary.

5 years agoRemove some unnecessary downcasts to int.
David Wells [Sun, 30 Dec 2018 15:38:32 +0000 (10:38 -0500)]
Remove some unnecessary downcasts to int.

This value is always used as an array index so we can keep it as std::ptrdiff_t
instead of downcasting to int.

Note that the line

    if (diag_find && std::fabs(...) == 0.0 ...)

checked the wrong thing: diag_find would have, if we did not find the value, be
set to col_indices + num_entries, not NULL.

5 years agoMerge pull request #7550 from davydden/feature/bfgs
Wolfgang Bangerth [Sat, 29 Dec 2018 15:57:27 +0000 (08:57 -0700)]
Merge pull request #7550 from davydden/feature/bfgs

add BFGS minimizer

5 years agoRestrict vector_tools/interpolate_with_material_id_02 7558/head
Daniel Arndt [Sat, 29 Dec 2018 13:53:50 +0000 (14:53 +0100)]
Restrict vector_tools/interpolate_with_material_id_02

5 years agoMerge pull request #7557 from masterleinad/test_enumerator_deprecate
David Wells [Sat, 29 Dec 2018 15:02:38 +0000 (10:02 -0500)]
Merge pull request #7557 from masterleinad/test_enumerator_deprecate

Also test enumerators in deprecation compiler checks

5 years agoAlso test enumerators in deprecation compiler checks 7557/head
Daniel Arndt [Sat, 29 Dec 2018 12:35:26 +0000 (13:35 +0100)]
Also test enumerators in deprecation compiler checks

5 years agoadd BFGS minimizer 7550/head
Denis Davydov [Mon, 24 Dec 2018 16:11:08 +0000 (17:11 +0100)]
add BFGS minimizer

5 years agoMerge pull request #7554 from drwells/add-missing-deprecated
Wolfgang Bangerth [Sat, 29 Dec 2018 00:40:46 +0000 (17:40 -0700)]
Merge pull request #7554 from drwells/add-missing-deprecated

Add a few missing DEAL_II_DEPRECATED attributes.

5 years agoMerge pull request #7527 from bangerth/fix-interpolate
Daniel Arndt [Fri, 28 Dec 2018 23:01:46 +0000 (00:01 +0100)]
Merge pull request #7527 from bangerth/fix-interpolate

Ensure that DoFs not touched by VectorTools::interpolate don't get set.

5 years agoAdd a few missing DEAL_II_DEPRECATED attributes. 7554/head
David Wells [Fri, 28 Dec 2018 21:01:34 +0000 (16:01 -0500)]
Add a few missing DEAL_II_DEPRECATED attributes.

5 years agoMerge pull request #7556 from drwells/doxygen-fixes
Wolfgang Bangerth [Fri, 28 Dec 2018 22:05:08 +0000 (15:05 -0700)]
Merge pull request #7556 from drwells/doxygen-fixes

Fix some minor doxygen issues.

5 years agoFix some minor doxygen issues. 7556/head
David Wells [Fri, 28 Dec 2018 21:23:14 +0000 (16:23 -0500)]
Fix some minor doxygen issues.

This commit adds missing text and improves some HTML.

5 years agoFix grid/distributed_compute_point_locations_02 7555/head
Daniel Arndt [Fri, 28 Dec 2018 20:34:04 +0000 (21:34 +0100)]
Fix grid/distributed_compute_point_locations_02

5 years agoImprove documentation of GridTools::find_closest_vertex
Daniel Arndt [Fri, 28 Dec 2018 20:31:54 +0000 (21:31 +0100)]
Improve documentation of GridTools::find_closest_vertex

5 years agoAdd test. 7527/head
Wolfgang Bangerth [Thu, 27 Dec 2018 18:27:46 +0000 (11:27 -0700)]
Add test.

5 years agoAdd one test.
Wolfgang Bangerth [Thu, 27 Dec 2018 18:23:45 +0000 (11:23 -0700)]
Add one test.

5 years agoEnsure that DoFs not touched by VectorTools::interpolate don't get set.
Wolfgang Bangerth [Wed, 12 Dec 2018 18:12:24 +0000 (11:12 -0700)]
Ensure that DoFs not touched by VectorTools::interpolate don't get set.

5 years agoMerge pull request #7553 from masterleinad/fix_typo
Martin Kronbichler [Fri, 28 Dec 2018 14:19:39 +0000 (15:19 +0100)]
Merge pull request #7553 from masterleinad/fix_typo

Fix a typo in matrix_free/fe_evaluation.h

5 years agoFix a typo 7553/head
Daniel Arndt [Fri, 28 Dec 2018 13:39:09 +0000 (14:39 +0100)]
Fix a typo

5 years agoMerge pull request #7552 from bangerth/cmake
Matthias Maier [Thu, 27 Dec 2018 15:58:31 +0000 (09:58 -0600)]
Merge pull request #7552 from bangerth/cmake

Clear the previously determined TBB version if we need to revert to the bundled one.

5 years agoClear the previously determined TBB version if we need to revert to the bundled one. 7552/head
Wolfgang Bangerth [Thu, 27 Dec 2018 15:38:57 +0000 (08:38 -0700)]
Clear the previously determined TBB version if we need to revert to the bundled one.

5 years agoMerge pull request #7544 from masterleinad/replace_trilinos_vector_partitioner
Daniel Arndt [Wed, 26 Dec 2018 07:30:30 +0000 (08:30 +0100)]
Merge pull request #7544 from masterleinad/replace_trilinos_vector_partitioner

Replace TrilinosWrappers::MPI:Vector::vector_partitioner

5 years agoMerge pull request #7539 from jodlbauer/master
Daniel Arndt [Tue, 25 Dec 2018 22:10:01 +0000 (23:10 +0100)]
Merge pull request #7539 from jodlbauer/master

Reinit blockvector only if required in matrix-free copy_to_mg

5 years agoExtend changelog entry 7544/head
Daniel Arndt [Tue, 25 Dec 2018 22:06:16 +0000 (23:06 +0100)]
Extend changelog entry

5 years agoChangelog entry
Daniel Arndt [Sat, 22 Dec 2018 23:45:30 +0000 (00:45 +0100)]
Changelog entry

5 years agoReplace vector_partitioner with thrilinos_partitioner
Daniel Arndt [Sat, 22 Dec 2018 14:33:52 +0000 (15:33 +0100)]
Replace vector_partitioner with thrilinos_partitioner

5 years agoMerge pull request #7538 from masterleinad/trilinos_clang_tidy
Daniel Arndt [Tue, 25 Dec 2018 22:01:12 +0000 (23:01 +0100)]
Merge pull request #7538 from masterleinad/trilinos_clang_tidy

Fix more Trilinos-related clang-tidy complains


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