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dealii.git
6 years agoMerge pull request #5125 from gassmoeller/add_particle_handler
Wolfgang Bangerth [Thu, 16 Nov 2017 22:14:57 +0000 (15:14 -0700)]
Merge pull request #5125 from gassmoeller/add_particle_handler

Add particle handler

6 years agoMerge pull request #5473 from jppelteret/ad-math_headers
Wolfgang Bangerth [Thu, 16 Nov 2017 20:58:42 +0000 (13:58 -0700)]
Merge pull request #5473 from jppelteret/ad-math_headers

Add math headers for AD numbers

6 years agoMerge pull request #5474 from jppelteret/ad-fe_values
Wolfgang Bangerth [Thu, 16 Nov 2017 19:59:35 +0000 (12:59 -0700)]
Merge pull request #5474 from jppelteret/ad-fe_values

Add support for AD calculations to FEValues functions

6 years agoMerge pull request #5117 from GivAlz/LocallyOwnedBBox
Bruno Turcksin [Thu, 16 Nov 2017 18:29:41 +0000 (13:29 -0500)]
Merge pull request #5117 from GivAlz/LocallyOwnedBBox

Compute bounding boxes approximating cells with a property (adding in grid_tools)

6 years agoMake serial case compile. Disable case without p4est. 5125/head
Rene Gassmoeller [Wed, 15 Nov 2017 21:04:13 +0000 (14:04 -0700)]
Make serial case compile. Disable case without p4est.

6 years agoTest to show that a zero-valued function can have non-zero derivatives. 5474/head
Jean-Paul Pelteret [Thu, 16 Nov 2017 16:13:43 +0000 (17:13 +0100)]
Test to show that a zero-valued function can have non-zero derivatives.

6 years agoRemove unnecessary ProductTypes and std::decay in FEValues functions
Jean-Paul Pelteret [Thu, 16 Nov 2017 08:08:47 +0000 (09:08 +0100)]
Remove unnecessary ProductTypes and std::decay in FEValues functions

With the current functionality my application of these two features in
the FEValues function is now overly defensive. So this effectively
reverts some of the changes made in #4951, as #4893 makes some use of
ProductType unnecessary and #5251 ensures compatible conversions between
numbers of all CV qualifications.

6 years agoAdd support for AD calculations to FEValues functions
Jean-Paul Pelteret [Thu, 16 Nov 2017 07:56:03 +0000 (08:56 +0100)]
Add support for AD calculations to FEValues functions

When using AD to automatically compute the linearisation of a residual, one cannot a-priori assume no sensitivity with respect to zero-valued degrees-of-freedom. This commit ensures that this calculation shortcut is not taken for AD numbers.

6 years agoRemove strict inclusion guards in unified AD header
Jean-Paul Pelteret [Thu, 16 Nov 2017 17:08:26 +0000 (18:08 +0100)]
Remove strict inclusion guards in unified AD header

6 years agoAdd Sacado math header 5473/head
Jean-Paul Pelteret [Thu, 16 Nov 2017 07:38:25 +0000 (08:38 +0100)]
Add Sacado math header

This adds some missing fundamental math functions for the supported
Sacado numbers.

6 years agoAdd Adol-C math header
Jean-Paul Pelteret [Thu, 16 Nov 2017 07:33:00 +0000 (08:33 +0100)]
Add Adol-C math header

This imports the Adol-C math operations into standard namespace. It
gives us the ability to use them (e.g. sqrt) within the Tensor class,
and it also allows the user to write generic code and switch between AD
number types.

6 years agoMerge pull request #5470 from tjhei/petsc_lu_doc2
Wolfgang Bangerth [Thu, 16 Nov 2017 15:01:43 +0000 (08:01 -0700)]
Merge pull request #5470 from tjhei/petsc_lu_doc2

update PETSc PreconditionLU documentation, take 2

6 years agoMerge pull request #5410 from kronbichler/improve_performance_transfinite
David Wells [Thu, 16 Nov 2017 13:45:25 +0000 (08:45 -0500)]
Merge pull request #5410 from kronbichler/improve_performance_transfinite

Performance improvement for transfinite interpolation manifold.

6 years agoMerge pull request #5392 from jppelteret/ad-numbers_and_type_traits
Jean-Paul Pelteret [Thu, 16 Nov 2017 07:26:39 +0000 (08:26 +0100)]
Merge pull request #5392 from jppelteret/ad-numbers_and_type_traits

 Implement type traits and helper classes for AD numbers

6 years agoMerge pull request #5471 from masterleinad/avoid_ub
Martin Kronbichler [Thu, 16 Nov 2017 07:06:28 +0000 (08:06 +0100)]
Merge pull request #5471 from masterleinad/avoid_ub

Guard some calls to memcpy, memset and memmove to avoid undefined behavior

6 years agoClean up code, fix comments by David. 5410/head
Martin Kronbichler [Wed, 15 Nov 2017 15:23:09 +0000 (16:23 +0100)]
Clean up code, fix comments by David.

6 years agoAdd tests for number traits classes: Sacado 5392/head
Jean-Paul Pelteret [Fri, 3 Nov 2017 19:15:41 +0000 (20:15 +0100)]
Add tests for number traits classes: Sacado

6 years agoAdd tests for number traits classes: Adol-C
Jean-Paul Pelteret [Fri, 3 Nov 2017 19:15:24 +0000 (20:15 +0100)]
Add tests for number traits classes: Adol-C

6 years agoImplement type traits and helper classes for Sacado numbers
Jean-Paul Pelteret [Fri, 3 Nov 2017 13:18:11 +0000 (14:18 +0100)]
Implement type traits and helper classes for Sacado numbers

6 years agoImplement type traits and helper classes for Adol-C numbers
Jean-Paul Pelteret [Fri, 3 Nov 2017 13:08:31 +0000 (14:08 +0100)]
Implement type traits and helper classes for Adol-C numbers

6 years agoAdd core headers for internally supported AD numbers
Jean-Paul Pelteret [Fri, 3 Nov 2017 12:47:04 +0000 (13:47 +0100)]
Add core headers for internally supported AD numbers

- Type codes
- Type traits

6 years agoAdd a unifying header for auto-differentation.
Jean-Paul Pelteret [Wed, 15 Nov 2017 12:44:12 +0000 (13:44 +0100)]
Add a unifying header for auto-differentation.

6 years agoAdd initial outline of documentation for the AD/SD module.
Jean-Paul Pelteret [Wed, 15 Nov 2017 12:37:18 +0000 (13:37 +0100)]
Add initial outline of documentation for the AD/SD module.

6 years agoMerge pull request #5472 from gassmoeller/fix_find_active_cell_around_point
Daniel Arndt [Thu, 16 Nov 2017 00:01:05 +0000 (01:01 +0100)]
Merge pull request #5472 from gassmoeller/fix_find_active_cell_around_point

Fix search for the cell of a vertex

6 years agoGuard some calls to memcpy, memset and memmove to avoid undefined behavior 5471/head
Daniel Arndt [Wed, 15 Nov 2017 15:50:21 +0000 (16:50 +0100)]
Guard some calls to memcpy, memset and memmove to avoid undefined behavior

6 years agoFix search for a vertex location 5472/head
Rene Gassmoeller [Wed, 15 Nov 2017 21:10:51 +0000 (14:10 -0700)]
Fix search for a vertex location

6 years agoAddress comments
Rene Gassmoeller [Tue, 14 Nov 2017 17:19:30 +0000 (10:19 -0700)]
Address comments

6 years agoMerge pull request #5457 from davydden/tests/sundials_fixes
Luca Heltai [Wed, 15 Nov 2017 16:37:17 +0000 (17:37 +0100)]
Merge pull request #5457 from davydden/tests/sundials_fixes

try to fix sundials tests

6 years agoupdate PETSc PreconditionLU documentation, take 2 5470/head
Timo Heister [Wed, 15 Nov 2017 14:59:58 +0000 (09:59 -0500)]
update PETSc PreconditionLU documentation, take 2

6 years agoMerge pull request #5467 from davydden/fix_deprecated_bug
Denis Davydov [Wed, 15 Nov 2017 12:08:55 +0000 (13:08 +0100)]
Merge pull request #5467 from davydden/fix_deprecated_bug

fix deprecation bug

6 years agofix deprecation bug 5467/head
Denis Davydov [Wed, 15 Nov 2017 10:52:52 +0000 (11:52 +0100)]
fix deprecation bug

6 years agoMerge pull request #5464 from vishalkenchan/rol/vector_adaptor
Daniel Arndt [Wed, 15 Nov 2017 09:05:59 +0000 (10:05 +0100)]
Merge pull request #5464 from vishalkenchan/rol/vector_adaptor

suppress use of ROL for older versions of Trilinos

6 years agoMerge pull request #5465 from sairajat/AssertionAdd
Daniel Arndt [Wed, 15 Nov 2017 09:05:13 +0000 (10:05 +0100)]
Merge pull request #5465 from sairajat/AssertionAdd

Added Assert in fe_values.h to ensure fe_values object is reinited to cell

6 years agoChecked Indentation 5465/head
RAJAT ARORA [Tue, 14 Nov 2017 18:18:10 +0000 (13:18 -0500)]
Checked Indentation

6 years agoMerge pull request #5463 from jppelteret/sacado_complex_rad_guard
Jean-Paul Pelteret [Tue, 14 Nov 2017 18:15:13 +0000 (19:15 +0100)]
Merge pull request #5463 from jppelteret/sacado_complex_rad_guard

Detect a compiler bug that prevents compilation of complex Sacado::Rad.

6 years agoAdded Assert in fe_values.h to ensure fe_values object is reinited to a cell
RAJAT ARORA [Tue, 14 Nov 2017 18:13:13 +0000 (13:13 -0500)]
Added Assert in fe_values.h to ensure fe_values object is reinited to a cell

6 years agorecommend enabling ROL package while building Trilinos 5464/head
vishalkenchan [Tue, 14 Nov 2017 17:45:24 +0000 (18:45 +0100)]
recommend enabling ROL package while building Trilinos

6 years agosuppress use of ROL for older versions of Trilinos
vishalkenchan [Tue, 14 Nov 2017 16:35:14 +0000 (17:35 +0100)]
suppress use of ROL for older versions of Trilinos

6 years agoMerge pull request #5462 from masterleinad/fix_test_project_03 5264/head
Denis Davydov [Tue, 14 Nov 2017 14:54:51 +0000 (15:54 +0100)]
Merge pull request #5462 from masterleinad/fix_test_project_03

Fix numerics/project_03

6 years agoMerge pull request #5459 from masterleinad/use_c++14_deprecated
Timo Heister [Tue, 14 Nov 2017 14:48:46 +0000 (09:48 -0500)]
Merge pull request #5459 from masterleinad/use_c++14_deprecated

Use c++14's [[deprecated]] if possible

6 years agoDetect a compiler bug that prevents compilation of complex Sacado::Rad. 5463/head
Jean-Paul Pelteret [Tue, 14 Nov 2017 14:31:45 +0000 (15:31 +0100)]
Detect a compiler bug that prevents compilation of complex Sacado::Rad.

6 years agoMerge pull request #5443 from davydden/vtu_binary
Wolfgang Bangerth [Tue, 14 Nov 2017 13:37:24 +0000 (06:37 -0700)]
Merge pull request #5443 from davydden/vtu_binary

filter XML binary output in some tests

6 years agoFix numerics/project_03 5462/head
Daniel Arndt [Tue, 14 Nov 2017 13:04:10 +0000 (14:04 +0100)]
Fix numerics/project_03

6 years agofix sundials tests 5457/head
Denis Davydov [Mon, 13 Nov 2017 20:59:12 +0000 (21:59 +0100)]
fix sundials tests

6 years agoMerge pull request #5461 from jppelteret/fix_5455
Jean-Paul Pelteret [Tue, 14 Nov 2017 08:32:38 +0000 (09:32 +0100)]
Merge pull request #5461 from jppelteret/fix_5455

Add header to tests using Sacado::Rad.

6 years agoUse [[deprecated]] if available 5459/head
Daniel Arndt [Mon, 13 Nov 2017 22:40:06 +0000 (23:40 +0100)]
Use [[deprecated]] if available

6 years agoAdd header to tests using Sacado::Rad. 5461/head
Jean-Paul Pelteret [Tue, 14 Nov 2017 06:35:45 +0000 (07:35 +0100)]
Add header to tests using Sacado::Rad.

For some older versions of Trilinos, the header for templated
Sacado::Rad numbers is missing from Sacado.hpp.

6 years agoMerge pull request #5385 from tjhei/prm_escape_latex
Wolfgang Bangerth [Tue, 14 Nov 2017 05:11:40 +0000 (22:11 -0700)]
Merge pull request #5385 from tjhei/prm_escape_latex

 escape characters in LaTeX format of ParameterHandler

6 years agoFix position of DEAL_II_DEPRECATED
Daniel Arndt [Mon, 13 Nov 2017 21:39:27 +0000 (22:39 +0100)]
Fix position of DEAL_II_DEPRECATED

6 years agoHide LevelInd, and add insert_particles(points)
Rene Gassmoeller [Sat, 11 Nov 2017 00:17:07 +0000 (17:17 -0700)]
Hide LevelInd, and add insert_particles(points)

6 years agofilter out binary data from XML output for some data_out tests 5443/head
Denis Davydov [Sun, 12 Nov 2017 19:47:02 +0000 (20:47 +0100)]
filter out binary data from XML output for some data_out tests

6 years agoMerge pull request #5452 from masterleinad/merge_grid_tools
Wolfgang Bangerth [Mon, 13 Nov 2017 17:13:31 +0000 (10:13 -0700)]
Merge pull request #5452 from masterleinad/merge_grid_tools

Merge parallel::GridTools into GridTools

6 years agocleanup a few data_out_base_vtu tests
Denis Davydov [Sun, 12 Nov 2017 19:20:05 +0000 (20:20 +0100)]
cleanup a few data_out_base_vtu tests

6 years agoUpdate changelog entries 5452/head
Daniel Arndt [Mon, 13 Nov 2017 14:56:33 +0000 (15:56 +0100)]
Update changelog entries

6 years agoReintroduce distributed/grid_tools.h for a deprecation warning
Daniel Arndt [Mon, 13 Nov 2017 14:51:39 +0000 (15:51 +0100)]
Reintroduce distributed/grid_tools.h for a deprecation warning

6 years agoMerge pull request #5447 from masterleinad/deprecate_vector_view
Wolfgang Bangerth [Mon, 13 Nov 2017 14:38:45 +0000 (07:38 -0700)]
Merge pull request #5447 from masterleinad/deprecate_vector_view

Deprecate VectorView

6 years agoMerge pull request #5453 from tjhei/petsc_lu_doc
Wolfgang Bangerth [Mon, 13 Nov 2017 14:35:26 +0000 (07:35 -0700)]
Merge pull request #5453 from tjhei/petsc_lu_doc

update documentation for PETSc PreconditionLU

6 years agoAdded method get_neighbor_type and EnumClass NeighborType in BoundingBox class. Added... 5117/head
Giovanni Alzetta [Thu, 28 Sep 2017 19:46:02 +0000 (19:46 +0000)]
Added method get_neighbor_type and EnumClass NeighborType in BoundingBox class. Added function compute_mesh_predicate_bounding_box to grid tools

6 years agoupdate documentation for PETSc PreconditionLU 5453/head
Timo Heister [Mon, 13 Nov 2017 14:05:16 +0000 (09:05 -0500)]
update documentation for PETSc PreconditionLU

6 years agoMerge distributed/grid_tools into grid/grid_tools
Daniel Arndt [Mon, 13 Nov 2017 11:37:24 +0000 (12:37 +0100)]
Merge distributed/grid_tools into grid/grid_tools

6 years agoRemove 'parallel' prefix in distributed/grid_tools
Daniel Arndt [Sun, 12 Nov 2017 20:35:40 +0000 (21:35 +0100)]
Remove 'parallel' prefix in distributed/grid_tools

6 years agoMerge pull request #5448 from bangerth/add-instantiation
Martin Kronbichler [Mon, 13 Nov 2017 13:33:35 +0000 (14:33 +0100)]
Merge pull request #5448 from bangerth/add-instantiation

Add a missing instantiation.

6 years agoMerge pull request #5444 from masterleinad/fix_interface_matrix_entry
Daniel Arndt [Mon, 13 Nov 2017 00:42:42 +0000 (01:42 +0100)]
Merge pull request #5444 from masterleinad/fix_interface_matrix_entry

Fix missing include file in multigrid/interface_matrix_entry_01

6 years agoMove deprecation declaration at the end 5447/head
Daniel Arndt [Sun, 12 Nov 2017 23:59:58 +0000 (00:59 +0100)]
Move deprecation declaration at the end

6 years agoAdd a test. 5448/head
Wolfgang Bangerth [Sun, 12 Nov 2017 23:30:29 +0000 (16:30 -0700)]
Add a test.

6 years agoAdd changelog entry.
Wolfgang Bangerth [Sun, 12 Nov 2017 23:13:41 +0000 (16:13 -0700)]
Add changelog entry.

6 years agoAdd missing instantiation of function.
Wolfgang Bangerth [Sun, 12 Nov 2017 23:13:34 +0000 (16:13 -0700)]
Add missing instantiation of function.

6 years agoDeprecate VectorView
Daniel Arndt [Sun, 12 Nov 2017 21:09:31 +0000 (22:09 +0100)]
Deprecate VectorView

6 years agoMerge pull request #5445 from drwells/update-gdbinit
Wolfgang Bangerth [Sun, 12 Nov 2017 21:11:19 +0000 (14:11 -0700)]
Merge pull request #5445 from drwells/update-gdbinit

Update the GDB pretty-printer.

6 years agoMerge pull request #5446 from drwells/convert-to-utf8
Wolfgang Bangerth [Sun, 12 Nov 2017 21:10:48 +0000 (14:10 -0700)]
Merge pull request #5446 from drwells/convert-to-utf8

Prefer UTF-8 to latin-1.

6 years agoPrefer UTF-8 to latin-1. 5446/head
David Wells [Sun, 12 Nov 2017 20:56:13 +0000 (15:56 -0500)]
Prefer UTF-8 to latin-1.

6 years agoUpdate the GDB pretty-printer. 5445/head
David Wells [Sun, 12 Nov 2017 20:52:15 +0000 (15:52 -0500)]
Update the GDB pretty-printer.

The data array variable was renamed from 'val' to 'values' in 2faae204c26.

6 years agoFix missing include filed in multigrid/interface_matrix_entry_01 5444/head
Daniel Arndt [Sun, 12 Nov 2017 20:35:40 +0000 (21:35 +0100)]
Fix missing include filed in multigrid/interface_matrix_entry_01

6 years agoMerge pull request #5442 from davydden/fix_illegal_character
David Wells [Sun, 12 Nov 2017 19:33:57 +0000 (14:33 -0500)]
Merge pull request #5442 from davydden/fix_illegal_character

fix illegal character (<F6> instead of oe)

6 years agofix illegal character (<F6> instead of oe) 5442/head
Denis Davydov [Sun, 12 Nov 2017 19:26:45 +0000 (20:26 +0100)]
fix illegal character (<F6> instead of oe)

6 years agoAdd changelog entry
Rene Gassmoeller [Fri, 10 Nov 2017 21:16:58 +0000 (14:16 -0700)]
Add changelog entry

6 years agoAddress some comments. Use map for send_recv_particles
Rene Gassmoeller [Fri, 10 Nov 2017 20:50:11 +0000 (13:50 -0700)]
Address some comments. Use map for send_recv_particles

6 years agoMerge pull request #5439 from kronbichler/extend_trilinos_direct_solver
Jean-Paul Pelteret [Fri, 10 Nov 2017 21:02:53 +0000 (22:02 +0100)]
Merge pull request #5439 from kronbichler/extend_trilinos_direct_solver

 Let Trilinos direct solver use given factorization with LA::distributed::Vector

6 years agomove to namespace 5385/head
Timo Heister [Fri, 10 Nov 2017 19:23:16 +0000 (14:23 -0500)]
move to namespace

6 years agoMerge pull request #5434 from tjhei/test_dos_2_unix
Timo Heister [Fri, 10 Nov 2017 18:03:17 +0000 (13:03 -0500)]
Merge pull request #5434 from tjhei/test_dos_2_unix

fix dos formatted files in contrib/utilities/indent

6 years agoMerge pull request #5380 from vishalkenchan/rol/vector_adaptor
Jean-Paul Pelteret [Fri, 10 Nov 2017 15:46:45 +0000 (16:46 +0100)]
Merge pull request #5380 from vishalkenchan/rol/vector_adaptor

Using Trilinos/ROL library

6 years agoAdd test. 5439/head
Martin Kronbichler [Fri, 10 Nov 2017 14:33:31 +0000 (15:33 +0100)]
Add test.

6 years agoChangelog
Martin Kronbichler [Fri, 10 Nov 2017 13:52:33 +0000 (14:52 +0100)]
Changelog

6 years agoEnable Trilinos direct solvers with LA::distributed::Vector.
Martin Kronbichler [Fri, 10 Nov 2017 13:50:09 +0000 (14:50 +0100)]
Enable Trilinos direct solvers with LA::distributed::Vector.

6 years agoadded rol tests 5380/head
vishalkenchan [Fri, 10 Nov 2017 09:15:36 +0000 (10:15 +0100)]
added rol tests

6 years agoadd a vector adaptor to use Trilinos/ROL library; added cmake variable DEAL_II_TRILIN...
vishalkenchan [Fri, 10 Nov 2017 09:15:12 +0000 (10:15 +0100)]
add a vector adaptor to use Trilinos/ROL library; added cmake variable DEAL_II_TRILINOS_WITH_ROL

6 years agoFurther speedup of transfinite interpolation.
Martin Kronbichler [Fri, 10 Nov 2017 08:35:50 +0000 (09:35 +0100)]
Further speedup of transfinite interpolation.

Try to use an initial guess for pull_back that is assuming cube-like geometries.
Skip some indirections inside compute_transfinite_interpolation.

6 years agoPerformance improvement for transfinite interpolation manifold.
Martin Kronbichler [Mon, 6 Nov 2017 12:21:06 +0000 (13:21 +0100)]
Performance improvement for transfinite interpolation manifold.

Pass initial point along to the push_forward_gradient call rather than re-computing it.
Use quasi-Newton method (Broyden's method) rather than full Newton with finite differences to reduce number of calls to the compute_transfinite_interpolation.

6 years agoIndent
Rene Gassmoeller [Fri, 10 Nov 2017 01:12:16 +0000 (18:12 -0700)]
Indent

6 years agofix dos formatted files in contrib/utilities/indent 5434/head
Timo Heister [Thu, 9 Nov 2017 18:58:51 +0000 (13:58 -0500)]
fix dos formatted files in contrib/utilities/indent

6 years agoAdd more tests
Rene Gassmoeller [Thu, 9 Nov 2017 18:42:00 +0000 (11:42 -0700)]
Add more tests

6 years agoMerge pull request #5408 from kronbichler/speedup_spherical_manifold
Martin Kronbichler [Thu, 9 Nov 2017 20:19:07 +0000 (21:19 +0100)]
Merge pull request #5408 from kronbichler/speedup_spherical_manifold

Speed up SphericalManifold::get_new_point

6 years agoMerge pull request #5433 from bangerth/fix-inst.in
Timo Heister [Thu, 9 Nov 2017 18:27:19 +0000 (13:27 -0500)]
Merge pull request #5433 from bangerth/fix-inst.in

Rename class groups in template-arguments.in.

6 years agoMerge pull request #5430 from bangerth/new-tests
Denis Davydov [Thu, 9 Nov 2017 17:30:45 +0000 (18:30 +0100)]
Merge pull request #5430 from bangerth/new-tests

Add tests for VectorTools::integrate_difference() using complex data types.

6 years agoAdd test
Rene Gassmoeller [Thu, 2 Nov 2017 23:30:24 +0000 (17:30 -0600)]
Add test

6 years agoFixes
Rene Gassmoeller [Mon, 16 Oct 2017 16:25:46 +0000 (10:25 -0600)]
Fixes

6 years agoAdd first particle handler test. Simplify update
Rene Gassmoeller [Fri, 13 Oct 2017 21:52:43 +0000 (15:52 -0600)]
Add first particle handler test. Simplify update

6 years agoAddress some comments
Rene Gassmoeller [Fri, 13 Oct 2017 21:06:02 +0000 (15:06 -0600)]
Address some comments

6 years agoRemove parallel::distributed where possible
Rene Gassmoeller [Fri, 13 Oct 2017 20:45:14 +0000 (14:45 -0600)]
Remove parallel::distributed where possible

6 years agoAdd ParticleHandler class
Rene Gassmoeller [Fri, 13 Oct 2017 20:03:17 +0000 (14:03 -0600)]
Add ParticleHandler class


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