]> https://gitweb.dealii.org/ - dealii.git/log
dealii.git
3 years agoLeave a note. 11520/head
Wolfgang Bangerth [Wed, 13 Jan 2021 23:39:06 +0000 (16:39 -0700)]
Leave a note.

3 years agoUse ReferenceCell::get_default_linear_mapping() in the .cc files.
Wolfgang Bangerth [Wed, 13 Jan 2021 23:38:54 +0000 (16:38 -0700)]
Use ReferenceCell::get_default_linear_mapping() in the .cc files.

3 years agoIntroduce ReferenceCell::get_default_linear_mapping() with triangulation argument.
Wolfgang Bangerth [Wed, 13 Jan 2021 23:38:38 +0000 (16:38 -0700)]
Introduce ReferenceCell::get_default_linear_mapping() with triangulation argument.

3 years agoMerge pull request #11509 from peterrum/permuation_assert
David Wells [Wed, 13 Jan 2021 13:18:13 +0000 (08:18 -0500)]
Merge pull request #11509 from peterrum/permuation_assert

Add an assert to ReferenceCell::compute_orientation()

3 years agoAdd an assert to ReferenceCell::compute_orientation() 11509/head
Peter Munch [Wed, 13 Jan 2021 10:45:22 +0000 (11:45 +0100)]
Add an assert to ReferenceCell::compute_orientation()

3 years agoMerge pull request #11500 from bangerth/doc
Timo Heister [Tue, 12 Jan 2021 16:05:10 +0000 (11:05 -0500)]
Merge pull request #11500 from bangerth/doc

Add some comments to VectorTools::interpolate_boundary_values().

3 years agoAlso point to the difference between nodal and non-nodal elements. 11500/head
Wolfgang Bangerth [Tue, 12 Jan 2021 00:51:31 +0000 (17:51 -0700)]
Also point to the difference between nodal and non-nodal elements.

3 years agoMerge pull request #11502 from mschreter/assert_tria_simplex_grid_generator
David Wells [Mon, 11 Jan 2021 20:18:33 +0000 (15:18 -0500)]
Merge pull request #11502 from mschreter/assert_tria_simplex_grid_generator

Assert type of coarse grid in p:d:T

3 years agoadd assert for unsupported p::d::T in the simplex grid generators 11502/head
Magdalena Schreter [Mon, 11 Jan 2021 11:01:33 +0000 (12:01 +0100)]
add assert for unsupported p::d::T in the simplex grid generators

assert is moved to distributed/tria.cc

3 years agoMerge pull request #11501 from peterrum/read_vtk_msh_mixed
David Wells [Mon, 11 Jan 2021 14:12:32 +0000 (09:12 -0500)]
Merge pull request #11501 from peterrum/read_vtk_msh_mixed

Enabling mixed meshes in GridIn::read_vkt() and read_msh()

3 years agoEnabling mixed meshes in GridIn::read_vkt() amd read_msh() 11501/head
Peter Munch [Sun, 10 Jan 2021 21:44:15 +0000 (22:44 +0100)]
Enabling mixed meshes in GridIn::read_vkt() amd read_msh()

3 years agoAdd some comments to VectorTools::interpolate_boundary_values().
Wolfgang Bangerth [Sat, 9 Jan 2021 22:32:43 +0000 (15:32 -0700)]
Add some comments to VectorTools::interpolate_boundary_values().

3 years agoMerge pull request #11499 from tjhei/doc_dsp
Wolfgang Bangerth [Sat, 9 Jan 2021 20:24:01 +0000 (13:24 -0700)]
Merge pull request #11499 from tjhei/doc_dsp

improve DynamicSparsityPattern usage documentation

3 years agoimprove DynamicSparsityPattern usage documentation 11499/head
Timo Heister [Sat, 9 Jan 2021 19:34:58 +0000 (14:34 -0500)]
improve DynamicSparsityPattern usage documentation

3 years agoMerge pull request #11498 from peterrum/typo
David Wells [Sat, 9 Jan 2021 14:42:17 +0000 (09:42 -0500)]
Merge pull request #11498 from peterrum/typo

Fix typo

3 years agoFix typo 11498/head
Peter Munch [Sat, 9 Jan 2021 07:39:53 +0000 (08:39 +0100)]
Fix typo

3 years agoMerge pull request #11479 from marcfehling/default-fe-series
Wolfgang Bangerth [Sat, 9 Jan 2021 04:32:25 +0000 (21:32 -0700)]
Merge pull request #11479 from marcfehling/default-fe-series

Adjusted settings for default FESeries::Legendre object.

3 years agoMerge pull request #11341 from Rombur/bicgstab
Wolfgang Bangerth [Fri, 8 Jan 2021 21:50:13 +0000 (14:50 -0700)]
Merge pull request #11341 from Rombur/bicgstab

Rework breakdown condition in BiCGSTAB

3 years agoMerge pull request #11493 from marcfehling/to-cell
Wolfgang Bangerth [Fri, 8 Jan 2021 21:43:08 +0000 (14:43 -0700)]
Merge pull request #11493 from marcfehling/to-cell

Replace deprecated CellId::to_cell().

3 years agoMerge pull request #11495 from drwells/fix-exodusii-test-output
Bruno Turcksin [Fri, 8 Jan 2021 21:26:47 +0000 (16:26 -0500)]
Merge pull request #11495 from drwells/fix-exodusii-test-output

Fix the VTK output in the exodusii test.

3 years agoFix the VTK output in the exodusii test. 11495/head
David Wells [Fri, 8 Jan 2021 15:19:54 +0000 (10:19 -0500)]
Fix the VTK output in the exodusii test.

The output for this test was generated before 2f788a5fdab, which changed (fixed)
the node numbering of pyramids. We need to apply the same permutation to this
output file.

3 years agoMerge pull request #11494 from drwells/fix-bbox-container-ctor
Bruno Turcksin [Fri, 8 Jan 2021 15:17:41 +0000 (10:17 -0500)]
Merge pull request #11494 from drwells/fix-bbox-container-ctor

Fix BoundingBox's Container ctor.

3 years agoMerge pull request #11475 from bangerth/74
David Wells [Fri, 8 Jan 2021 03:30:12 +0000 (22:30 -0500)]
Merge pull request #11475 from bangerth/74

Clarify what the picture shows in step-74.

3 years agoFix BoundingBox's Container ctor. 11494/head
David Wells [Fri, 8 Jan 2021 03:09:16 +0000 (22:09 -0500)]
Fix BoundingBox's Container ctor.

I get inscrutably long boost errors right now (which was partially fixed in
13bc2f8a021) about boost not being able to figure out type conversions. Lets
just roll our own BoundingBox function to fix the problem here and with other
versions of boost.

3 years agoReplace deprecated CellId::to_cell(). 11493/head
Marc Fehling [Fri, 8 Jan 2021 03:04:34 +0000 (20:04 -0700)]
Replace deprecated CellId::to_cell().

3 years agoMerge pull request #11492 from bangerth/const-2
Timo Heister [Fri, 8 Jan 2021 02:10:23 +0000 (21:10 -0500)]
Merge pull request #11492 from bangerth/const-2

Make one variable 'const'.

3 years agoMerge pull request #11486 from adamqc/fix-distribute_dofs
Timo Heister [Thu, 7 Jan 2021 22:10:15 +0000 (17:10 -0500)]
Merge pull request #11486 from adamqc/fix-distribute_dofs

Fix bug in DoFHandler::distribute_dofs

3 years agoMerge pull request #11491 from bangerth/const
Timo Heister [Thu, 7 Jan 2021 22:08:22 +0000 (17:08 -0500)]
Merge pull request #11491 from bangerth/const

Clean up some in function_lib.cc.

3 years agoMerge pull request #11468 from bangerth/L-function
Timo Heister [Thu, 7 Jan 2021 22:02:50 +0000 (17:02 -0500)]
Merge pull request #11468 from bangerth/L-function

Better explain the purpose of the L-singularity function.

3 years agoMerge pull request #11378 from bangerth/figure
Peter Munch [Thu, 7 Jan 2021 17:45:42 +0000 (18:45 +0100)]
Merge pull request #11378 from bangerth/figure

Link in the correct figure.

3 years agoMake one variable 'const'. 11492/head
Wolfgang Bangerth [Thu, 7 Jan 2021 16:23:36 +0000 (09:23 -0700)]
Make one variable 'const'.

3 years agoClean up some in function_lib.cc. 11491/head
Wolfgang Bangerth [Thu, 7 Jan 2021 16:22:01 +0000 (09:22 -0700)]
Clean up some in function_lib.cc.

Specifically, add 'const' to a lot of variables. Also rename r2 to r_squared.

3 years agoBetter explain the purpose of the L-singularity function. 11468/head
Wolfgang Bangerth [Tue, 5 Jan 2021 00:39:06 +0000 (17:39 -0700)]
Better explain the purpose of the L-singularity function.

3 years agoMerge pull request #11488 from marcfehling/update-27-2
Wolfgang Bangerth [Thu, 7 Jan 2021 14:38:37 +0000 (07:38 -0700)]
Merge pull request #11488 from marcfehling/update-27-2

step-27: Changed relative threshold. Updated output.

3 years agoFix bug in distribute_dofs 11486/head
Ce Qin [Wed, 6 Jan 2021 12:09:15 +0000 (20:09 +0800)]
Fix bug in distribute_dofs

3 years agostep-27: Changed relative threshold. Updated output. 11488/head
Marc Fehling [Thu, 7 Jan 2021 01:31:47 +0000 (18:31 -0700)]
step-27: Changed relative threshold. Updated output.

3 years agoMerge pull request #11418 from marcfehling/update-27
Wolfgang Bangerth [Thu, 7 Jan 2021 05:21:58 +0000 (22:21 -0700)]
Merge pull request #11418 from marcfehling/update-27

step-27: Updated to new interface.

3 years agoMerge pull request #11422 from peterrum/simplex_compute_embedding_matrices
David Wells [Wed, 6 Jan 2021 15:48:50 +0000 (10:48 -0500)]
Merge pull request #11422 from peterrum/simplex_compute_embedding_matrices

Work on compute_embedding_matrices() for simplex

3 years agoMerge pull request #11392 from bangerth/serialize-2
Bruno Turcksin [Wed, 6 Jan 2021 14:45:13 +0000 (09:45 -0500)]
Merge pull request #11392 from bangerth/serialize-2

Better document serialization functions.

3 years agoMerge pull request #11477 from zjiaqi2018/step-74-fix
Daniel Arndt [Wed, 6 Jan 2021 05:38:05 +0000 (00:38 -0500)]
Merge pull request #11477 from zjiaqi2018/step-74-fix

step-74 fix: energy norm description

3 years agoMerge pull request #11458 from peterrum/simplex_step74
Daniel Arndt [Wed, 6 Jan 2021 05:37:49 +0000 (00:37 -0500)]
Merge pull request #11458 from peterrum/simplex_step74

Convert step-74 to a simplex test

3 years agoMerge pull request #11457 from peterrum/simplex_step_12
Daniel Arndt [Wed, 6 Jan 2021 05:37:38 +0000 (00:37 -0500)]
Merge pull request #11457 from peterrum/simplex_step_12

Convert step-12 to a simplex test

3 years agoMerge pull request #11474 from bangerth/bubbles
Daniel Arndt [Wed, 6 Jan 2021 05:37:28 +0000 (00:37 -0500)]
Merge pull request #11474 from bangerth/bubbles

Clarify a number of comments around FE_Q_Bubbles.

3 years agostep-27: Updated to new interface. 11418/head
Marc Fehling [Mon, 9 Sep 2019 16:53:14 +0000 (18:53 +0200)]
step-27: Updated to new interface.

3 years agoAdjusted settings for default FESeries::Legendre object. 11479/head
Marc Fehling [Wed, 6 Jan 2021 04:14:59 +0000 (21:14 -0700)]
Adjusted settings for default FESeries::Legendre object.

3 years agoMerge pull request #11388 from tjhei/interpolated_data_access
Wolfgang Bangerth [Wed, 6 Jan 2021 03:59:43 +0000 (20:59 -0700)]
Merge pull request #11388 from tjhei/interpolated_data_access

Allow read access to data in Interpolated*Function

3 years agoMerge pull request #11446 from marcfehling/cell-id-08
Wolfgang Bangerth [Wed, 6 Jan 2021 03:53:08 +0000 (20:53 -0700)]
Merge pull request #11446 from marcfehling/cell-id-08

Update grid/cell_id_08 output.

3 years agoMerge pull request #11449 from peterrum/simplex_step_02
Wolfgang Bangerth [Wed, 6 Jan 2021 03:49:44 +0000 (20:49 -0700)]
Merge pull request #11449 from peterrum/simplex_step_02

Convert step-2 to a simplex test

3 years agoMerge pull request #11476 from bangerth/new
Timo Heister [Wed, 6 Jan 2021 01:33:58 +0000 (20:33 -0500)]
Merge pull request #11476 from bangerth/new

Avoid using bare 'new'.

3 years agoMerge pull request #11471 from marcfehling/default-fe-series
Daniel Arndt [Tue, 5 Jan 2021 23:15:54 +0000 (18:15 -0500)]
Merge pull request #11471 from marcfehling/default-fe-series

Adjusted settings for default FESeries object.

3 years agoadd energy norm description 11477/head
Jiaqi Zhang [Tue, 5 Jan 2021 22:38:50 +0000 (17:38 -0500)]
add energy norm description

3 years agoConvert step-74 to a simplex test 11458/head
Peter Munch [Sun, 3 Jan 2021 10:35:35 +0000 (11:35 +0100)]
Convert step-74 to a simplex test

3 years agoConvert step-12 to a simplex test 11457/head
Peter Munch [Sat, 2 Jan 2021 23:26:40 +0000 (00:26 +0100)]
Convert step-12 to a simplex test

3 years agoConvert step-2 to a simplex test 11449/head
Peter Munch [Thu, 31 Dec 2020 12:15:51 +0000 (13:15 +0100)]
Convert step-2 to a simplex test

3 years agoClarify a number of comments around FE_Q_Bubbles. 11474/head
Wolfgang Bangerth [Tue, 5 Jan 2021 17:13:23 +0000 (10:13 -0700)]
Clarify a number of comments around FE_Q_Bubbles.

3 years agoAvoid using bare 'new'. 11476/head
Wolfgang Bangerth [Tue, 5 Jan 2021 21:19:50 +0000 (14:19 -0700)]
Avoid using bare 'new'.

3 years agoMerge pull request #11456 from peterrum/simplex_tria_refinement_neighbors
Wolfgang Bangerth [Tue, 5 Jan 2021 21:14:13 +0000 (14:14 -0700)]
Merge pull request #11456 from peterrum/simplex_tria_refinement_neighbors

Add a version of update_neighbors() for simplex meshes

3 years agoMerge pull request #11473 from bangerth/pp-7
Martin Kronbichler [Tue, 5 Jan 2021 20:14:20 +0000 (21:14 +0100)]
Merge pull request #11473 from bangerth/pp-7

Minor adjustments

3 years agoClarify what the picture shows in step-74. 11475/head
Wolfgang Bangerth [Tue, 5 Jan 2021 17:19:33 +0000 (10:19 -0700)]
Clarify what the picture shows in step-74.

3 years agoAdjust spacing. 11473/head
Wolfgang Bangerth [Tue, 5 Jan 2021 17:12:31 +0000 (10:12 -0700)]
Adjust spacing.

3 years agoStore value, not reference, in a local variable.
Wolfgang Bangerth [Tue, 5 Jan 2021 17:12:54 +0000 (10:12 -0700)]
Store value, not reference, in a local variable.

3 years agoMerge pull request #11460 from cpraveen/step-26
Peter Munch [Tue, 5 Jan 2021 08:07:59 +0000 (09:07 +0100)]
Merge pull request #11460 from cpraveen/step-26

step-26: Reset time and timestep_number during pre refinement steps

3 years agoMerge pull request #11470 from marcfehling/gsl-check
Peter Munch [Tue, 5 Jan 2021 08:01:44 +0000 (09:01 +0100)]
Merge pull request #11470 from marcfehling/gsl-check

GSL no longer requirement for FESeries::Legendre in tests.

3 years agoAdjusted settings for default FESeries object. 11471/head
Marc Fehling [Tue, 5 Jan 2021 05:55:29 +0000 (22:55 -0700)]
Adjusted settings for default FESeries object.

3 years agoMerge pull request #11467 from bangerth/step-74
Daniel Arndt [Tue, 5 Jan 2021 05:16:03 +0000 (00:16 -0500)]
Merge pull request #11467 from bangerth/step-74

3 years agoGSL no longer requirement for FESeries::Legendre in tests. 11470/head
Marc Fehling [Tue, 5 Jan 2021 04:26:04 +0000 (21:26 -0700)]
GSL no longer requirement for FESeries::Legendre in tests.

3 years agoMerge pull request #11454 from peterrum/simplex_flatten_triangulation
Wolfgang Bangerth [Tue, 5 Jan 2021 04:20:13 +0000 (21:20 -0700)]
Merge pull request #11454 from peterrum/simplex_flatten_triangulation

Generalize GridGenerator::flatten_triangulation for simplex meshes

3 years agoMerge pull request #11469 from tjhei/reference_74
Wolfgang Bangerth [Tue, 5 Jan 2021 03:56:31 +0000 (20:56 -0700)]
Merge pull request #11469 from tjhei/reference_74

add step-74 to tutorial page

3 years agoReset time and timestep_number during pre refinement steps 11460/head
Praveen C [Mon, 4 Jan 2021 04:17:50 +0000 (09:47 +0530)]
Reset time and timestep_number during pre refinement steps

Otherwise, the pre-refinement is performed only once. See https://github.com/dealii/dealii/issues/10715

3 years agoadd step-74 to tutorial page 11469/head
Timo Heister [Tue, 5 Jan 2021 01:28:02 +0000 (20:28 -0500)]
add step-74 to tutorial page

3 years agoUpdate text and code of step-74. 11467/head
Wolfgang Bangerth [Tue, 5 Jan 2021 00:36:48 +0000 (17:36 -0700)]
Update text and code of step-74.

3 years agoLeave a reference to step-74.
Wolfgang Bangerth [Tue, 5 Jan 2021 00:35:55 +0000 (17:35 -0700)]
Leave a reference to step-74.

3 years agoFix spelling.
Wolfgang Bangerth [Mon, 4 Jan 2021 23:43:18 +0000 (16:43 -0700)]
Fix spelling.

3 years agoAdd references to step-47.
Wolfgang Bangerth [Mon, 4 Jan 2021 23:10:54 +0000 (16:10 -0700)]
Add references to step-47.

3 years agoBe consistent in the spelling and use of 'unsigned int'.
Wolfgang Bangerth [Mon, 4 Jan 2021 22:26:52 +0000 (15:26 -0700)]
Be consistent in the spelling and use of 'unsigned int'.

3 years agoMinor changes
Peter Munch [Sun, 3 Jan 2021 11:45:32 +0000 (12:45 +0100)]
Minor changes

3 years agoMerge pull request #10932 from zjiaqi2018/step-74
Wolfgang Bangerth [Mon, 4 Jan 2021 22:13:31 +0000 (15:13 -0700)]
Merge pull request #10932 from zjiaqi2018/step-74

Step 74: Symmetric interior penalty Galerkin (SIPG) method for Poisson's equation

3 years agoMerge pull request #11415 from Rombur/disable_extra
David Wells [Mon, 4 Jan 2021 15:01:04 +0000 (10:01 -0500)]
Merge pull request #11415 from Rombur/disable_extra

Ignore deprecated-volatile warning when disabling exta diagnostic

3 years agoMerge pull request #11453 from peterrum/use_vector_data_exchanger_full_remove
Martin Kronbichler [Mon, 4 Jan 2021 12:47:05 +0000 (13:47 +0100)]
Merge pull request #11453 from peterrum/use_vector_data_exchanger_full_remove

Remove MF::AD::use_vector_data_exchanger_full

3 years agoAdd a version of update_neighbors() for simplex meshes 11456/head
Peter Munch [Sat, 2 Jan 2021 22:25:58 +0000 (23:25 +0100)]
Add a version of update_neighbors() for simplex meshes

3 years agoMerge pull request #11455 from peterrum/step-12-quad
Peter Munch [Sun, 3 Jan 2021 07:12:11 +0000 (08:12 +0100)]
Merge pull request #11455 from peterrum/step-12-quad

Step-12: select quadrature at a central place

3 years agoStep-12: select quadrature at a central place 11455/head
Peter Munch [Sat, 2 Jan 2021 10:55:40 +0000 (11:55 +0100)]
Step-12: select quadrature at a central place

3 years agoGeneralize GridGenerator::flatten_triangulation for simplex meshes 11454/head
Peter Munch [Sat, 2 Jan 2021 22:38:22 +0000 (23:38 +0100)]
Generalize GridGenerator::flatten_triangulation for simplex meshes

3 years agoRemove use_vector_data_exchanger_full 11453/head
Peter Munch [Sat, 2 Jan 2021 10:25:58 +0000 (11:25 +0100)]
Remove use_vector_data_exchanger_full

3 years agoMerge pull request #11445 from marcfehling/hp-cell-weights
Peter Munch [Sat, 2 Jan 2021 10:09:12 +0000 (11:09 +0100)]
Merge pull request #11445 from marcfehling/hp-cell-weights

Minor change to CellWeights exception handling.

3 years agoMinor change to CellWeights exception handling. 11445/head
Marc Fehling [Thu, 31 Dec 2020 02:19:26 +0000 (19:19 -0700)]
Minor change to CellWeights exception handling.

3 years agoBetter document serialization functions. 11392/head
Wolfgang Bangerth [Thu, 17 Dec 2020 21:38:47 +0000 (14:38 -0700)]
Better document serialization functions.

Specifically, equip all of them with a link to the BOOST library.

3 years agoWork on compute_embedding_matrices for simplex 11422/head
Peter Munch [Sat, 26 Dec 2020 21:55:06 +0000 (22:55 +0100)]
Work on compute_embedding_matrices for simplex

3 years agoMerge pull request #11452 from masterleinad/fix_redefinition_default_argument
Daniel Arndt [Thu, 31 Dec 2020 23:37:15 +0000 (18:37 -0500)]
Merge pull request #11452 from masterleinad/fix_redefinition_default_argument

Fix redefinition of default argument in test

3 years agoFix redefinition of default argument in test 11452/head
Daniel Arndt [Thu, 31 Dec 2020 21:22:40 +0000 (16:22 -0500)]
Fix redefinition of default argument in test

3 years agoMerge pull request #11444 from drwells/refactor-hdf5-abort
Wolfgang Bangerth [Thu, 31 Dec 2020 20:58:11 +0000 (13:58 -0700)]
Merge pull request #11444 from drwells/refactor-hdf5-abort

Refactor the HDF5 abort code.

3 years agoMerge pull request #11447 from marcfehling/hyper-line
David Wells [Thu, 31 Dec 2020 20:57:45 +0000 (15:57 -0500)]
Merge pull request #11447 from marcfehling/hyper-line

Utility grid generator function `hyper_line` for tests.

3 years agoMerge pull request #11428 from peterrum/simplex_get_projection_matrix
David Wells [Thu, 31 Dec 2020 20:57:18 +0000 (15:57 -0500)]
Merge pull request #11428 from peterrum/simplex_get_projection_matrix

FETools::get_projection_matrix for simplices

3 years agoMerge pull request #11371 from peterrum/q_collection_fe_interface_values
David Wells [Thu, 31 Dec 2020 18:30:33 +0000 (13:30 -0500)]
Merge pull request #11371 from peterrum/q_collection_fe_interface_values

FEInterfaceValues: pass to the constructor hp::QCollection

3 years agoMerge pull request #11318 from peterrum/cg_reshuffle
David Wells [Thu, 31 Dec 2020 17:21:43 +0000 (12:21 -0500)]
Merge pull request #11318 from peterrum/cg_reshuffle

Reshuffle code in SolverCG

3 years agoFETools::get_projection_matrix for simplices 11428/head
Peter Munch [Mon, 28 Dec 2020 10:59:23 +0000 (11:59 +0100)]
FETools::get_projection_matrix for simplices

3 years agoMerge pull request #11442 from bangerth/pp-5
Peter Munch [Thu, 31 Dec 2020 05:28:52 +0000 (06:28 +0100)]
Merge pull request #11442 from bangerth/pp-5

Make a test more verbose.

3 years agoUtility grid hyper_line for tests. 11447/head
Marc Fehling [Thu, 31 Dec 2020 03:48:18 +0000 (20:48 -0700)]
Utility grid hyper_line for tests.

3 years agoUpdate grid/cell_id_08 output. 11446/head
Marc Fehling [Thu, 31 Dec 2020 03:06:38 +0000 (20:06 -0700)]
Update grid/cell_id_08 output.

3 years agoRefactor the HDF5 abort code. 11444/head
David Wells [Thu, 31 Dec 2020 01:28:40 +0000 (20:28 -0500)]
Refactor the HDF5 abort code.


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