[dolfin] 01/08: Update upstream source from tag 'upstream/2017.2.0.post0'

Drew Parsons dparsons at moszumanska.debian.org
Sun Jan 21 15:00:12 UTC 2018


This is an automated email from the git hooks/post-receive script.

dparsons pushed a commit to tag experimental/2017.2.0.post0-1exp1
in repository dolfin.

commit 1b7b3d7aa8c59cbefcb6122512dd8f6e59c56d17
Merge: 2e61a9e 3907d05
Author: Drew Parsons <dparsons at debian.org>
Date:   Sun Jan 21 19:31:04 2018 +0800

    Update upstream source from tag 'upstream/2017.2.0.post0'
    
    Update to upstream version '2017.2.0.post0'
    with Debian dir 3b94d35c7e0c0fb1a18ffa60f6c803c9cb9370b3

 .circleci/config.yml                               |    32 +-
 CMakeLists.txt                                     |    54 +-
 ChangeLog.rst                                      |    13 +
 bench/fem/jit/python/bench_fem_jit_python          |     2 +-
 cmake/modules/FindGMP.cmake                        |    19 +
 cmake/modules/FindMPFR.cmake                       |    83 +
 cmake/templates/dolfin.conf.in                     |     3 -
 demo/CMakeLists.txt                                |     2 +-
 demo/documented/bcs/python/demo_bcs.py             |     2 +-
 demo/documented/biharmonic/cpp/Biharmonic.ufl.rst  |     2 +-
 .../biharmonic/python/demo_biharmonic.py.rst       |     2 +-
 .../documented/cahn-hilliard/cpp/documentation.rst |     3 +-
 demo/documented/cahn-hilliard/cpp/main.cpp         |     4 +-
 .../cahn-hilliard/python/demo_cahn-hilliard.py.rst |     2 +-
 demo/documented/neumann-poisson/cpp/main.cpp       |     3 +-
 .../python/demo_neumann-poisson.py.rst             |     6 +-
 demo/documented/poisson/cpp/main.cpp.rst           |     3 +-
 demo/documented/stokes-iterative/cpp/main.cpp      |     3 +-
 .../python/demo_stokes-iterative.py.rst            |     6 +-
 .../python/demo_subdomains-poisson.py              |     4 +-
 .../subdomains-poisson/python/documentation.rst    |    21 +-
 .../python/demo_tensor-weighted-poisson.py         |    15 +-
 .../python/demo_advection-diffusion.py             |     2 +-
 .../auto-adaptive-navier-stokes/cpp/main.cpp       |     4 +-
 .../buckling-tao/python/demo_buckling-tao.py       |     2 +-
 .../python/demo_collision-detection.py             |     2 +-
 .../curl-curl/python/demo_curl-curl.py             |     2 +-
 .../cpp/AdvectionDiffusion.ufl                     |     2 +-
 .../python/demo_dg-advection-diffusion.py          |     2 +-
 demo/undocumented/dg-poisson/cpp/Poisson.ufl       |     2 +-
 demo/undocumented/dg-poisson/cpp/main.cpp          |     2 +-
 .../dg-poisson/python/demo_dg-poisson.py           |     4 +-
 demo/undocumented/elasticity/cpp/main.cpp          |     4 +-
 .../elasticity/python/demo_elasticity.py           |     2 +-
 .../ghost-mesh/python/demo_ghost-mesh.py           |     2 +-
 demo/undocumented/lift-drag/cpp/main.cpp           |     2 +-
 .../lift-drag/python/demo_lift-drag.py             |     2 +-
 demo/undocumented/multimesh-3d/cpp/CMakeLists.txt  |    38 +
 .../multimesh-3d/cpp/MultiMeshH10Norm.ufl          |    20 +
 .../multimesh-3d/cpp/MultiMeshL2Norm.ufl           |    20 +
 .../cpp/MultiMeshPoisson.ufl                       |     9 +-
 demo/undocumented/multimesh-3d/cpp/main.cpp        |   224 +
 .../multimesh-poisson/cpp/MultiMeshPoisson.ufl     |    10 +-
 .../undocumented/multimesh-poisson/cpp/P1.ufl      |    24 +-
 demo/undocumented/multimesh-poisson/cpp/main.cpp   |    51 +-
 .../python/demo_multimesh-poisson.py               |    53 +-
 demo/undocumented/multimesh-quadrature/cpp/README  |     2 +
 .../propeller_2d_coarse.xml.gz                     |   Bin
 .../propeller_2d_fine.xml.gz                       |   Bin
 .../python/demo_multimesh-quadrature.py            |   147 +
 .../multimesh-stokes/cpp/MultiMeshStokes.ufl       |    10 +-
 demo/undocumented/multimesh-stokes/cpp/Stokes.ufl  |    52 -
 demo/undocumented/multimesh-stokes/cpp/main.cpp    |    42 +-
 demo/undocumented/multimesh-stokes/cpp/reference.h |    49 -
 .../python/demo_multimesh-stokes.py                |    52 +-
 .../multimesh/python/demo_multimesh.py             |   138 -
 .../python/demo_multistage-solver.py               |     2 +-
 .../python/demo_overlapping-regions.py             |     2 +-
 demo/undocumented/parallel-refinement/cpp/main.cpp |    16 +-
 .../python/demo_parallel-refinement.py             |     8 +-
 .../point-integral/python/demo_point-integral.py   |     2 +-
 .../refinement/python/demo_refinement.py           |     2 +-
 doc/source/conf.py                                 |     4 +-
 dolfin/CMakeLists.txt                              |    10 +
 dolfin/common/Variable.h                           |     2 +-
 dolfin/fem/AssemblerBase.cpp                       |    62 +-
 dolfin/fem/DirichletBC.cpp                         |     2 +-
 dolfin/fem/DiscreteOperators.cpp                   |     4 +-
 dolfin/fem/DofMap.h                                |     2 +-
 dolfin/fem/DofMapBuilder.cpp                       |     8 +-
 dolfin/fem/DofMapBuilder.h                         |     1 +
 dolfin/fem/MultiMeshAssembler.cpp                  |   219 +-
 dolfin/fem/MultiMeshAssembler.h                    |     3 +
 dolfin/fem/MultiMeshDirichletBC.cpp                |    47 +
 dolfin/fem/MultiMeshDirichletBC.h                  |    18 +-
 dolfin/fem/MultiMeshDofMap.cpp                     |    47 +
 dolfin/fem/MultiMeshDofMap.h                       |     6 +
 dolfin/fem/MultiMeshForm.cpp                       |    28 +
 dolfin/fem/MultiMeshForm.h                         |    18 +
 dolfin/fem/PETScDMCollection.cpp                   |     1 +
 dolfin/fem/PETScDMCollection.h                     |     2 +-
 dolfin/fem/UFC.h                                   |     7 +-
 dolfin/fem/fem_utils.cpp                           |     1 +
 dolfin/function/Function.cpp                       |     9 +-
 dolfin/function/FunctionAssigner.cpp               |     1 +
 dolfin/function/FunctionSpace.h                    |     3 +-
 dolfin/function/MultiMeshCoefficientAssigner.cpp   |     7 +-
 dolfin/function/MultiMeshCoefficientAssigner.h     |     2 +-
 dolfin/function/MultiMeshFunction.cpp              |   165 +-
 dolfin/function/MultiMeshFunction.h                |    62 +
 dolfin/function/MultiMeshFunctionSpace.cpp         |    33 +-
 dolfin/function/MultiMeshFunctionSpace.h           |     7 +-
 dolfin/generation/BoxMesh.cpp                      |    90 +-
 dolfin/generation/BoxMesh.h                        |    29 +-
 dolfin/generation/CMakeLists.txt                   |     4 -
 dolfin/generation/IntervalMesh.cpp                 |     2 +-
 dolfin/generation/RectangleMesh.cpp                |    77 +-
 dolfin/generation/RectangleMesh.h                  |    42 +-
 dolfin/generation/SphericalShellMesh.cpp           |     2 +-
 dolfin/generation/UnitCubeMesh.h                   |    32 +-
 dolfin/generation/UnitDiscMesh.cpp                 |     2 +-
 dolfin/generation/UnitHexMesh.cpp                  |   111 -
 dolfin/generation/UnitHexMesh.h                    |    56 -
 dolfin/generation/UnitQuadMesh.cpp                 |    96 -
 dolfin/generation/UnitQuadMesh.h                   |    59 -
 dolfin/generation/UnitSquareMesh.h                 |    39 +-
 dolfin/generation/UnitTetrahedronMesh.cpp          |     2 +-
 dolfin/generation/UnitTriangleMesh.cpp             |     2 +-
 dolfin/generation/dolfin_generation.h              |     2 -
 dolfin/geometry/BoundingBoxTree2D.h                |     6 +-
 dolfin/geometry/CGALExactArithmetic.h              |  1152 ++
 dolfin/geometry/CMakeLists.txt                     |    17 +-
 dolfin/geometry/CollisionDetection.cpp             |  1158 --
 dolfin/geometry/CollisionDetection.h               |   296 -
 dolfin/geometry/CollisionPredicates.cpp            |  1053 ++
 dolfin/geometry/CollisionPredicates.h              |   316 +
 dolfin/geometry/ConvexTriangulation.cpp            |   603 +
 dolfin/geometry/ConvexTriangulation.h              |    84 +
 dolfin/geometry/GenericBoundingBoxTree.cpp         |    14 +-
 dolfin/geometry/GeometryDebugging.cpp              |   151 +
 dolfin/geometry/GeometryDebugging.h                |    83 +
 dolfin/geometry/GeometryPredicates.cpp             |   214 +
 dolfin/geometry/GeometryPredicates.h               |    70 +
 dolfin/geometry/GeometryTools.h                    |   120 +
 dolfin/geometry/IntersectionConstruction.cpp       |   862 ++
 dolfin/geometry/IntersectionConstruction.h         |   292 +
 dolfin/geometry/IntersectionTriangulation.cpp      |  1365 ---
 dolfin/geometry/IntersectionTriangulation.h        |   214 -
 dolfin/geometry/Point.h                            |    10 +-
 dolfin/geometry/SimplexQuadrature.cpp              |  3944 ++++++-
 dolfin/geometry/SimplexQuadrature.h                |   237 +-
 dolfin/geometry/dolfin_geometry.h                  |     1 +
 dolfin/geometry/intersect.cpp                      |    12 +-
 dolfin/geometry/predicates.cpp                     |  2372 ++++
 dolfin/geometry/predicates.h                       |    59 +
 dolfin/io/HDF5File.cpp                             |    18 +-
 dolfin/io/HDF5Utility.cpp                          |     4 +-
 dolfin/io/VTKWriter.cpp                            |    12 +-
 dolfin/io/X3DFile.cpp                              |     4 +-
 dolfin/io/XDMFFile.cpp                             |    43 +-
 dolfin/io/XMLMesh.cpp                              |     6 +-
 dolfin/la/EigenVector.cpp                          |    12 +-
 dolfin/la/GenericMatrix.cpp                        |     4 +-
 dolfin/la/GenericMatrix.h                          |     5 +-
 dolfin/la/PETScObject.h                            |     1 +
 dolfin/la/SLEPcEigenSolver.cpp                     |    41 +-
 dolfin/la/SLEPcEigenSolver.h                       |     3 -
 dolfin/log/Logger.cpp                              |    17 +-
 dolfin/log/Logger.h                                |     5 +-
 dolfin/log/log.cpp                                 |     5 +
 dolfin/log/log.h                                   |     3 +
 dolfin/mesh/BoundaryComputation.cpp                |     6 +-
 dolfin/mesh/CMakeLists.txt                         |     1 +
 dolfin/{geometry/intersect.cpp => mesh/Cell.cpp}   |    32 +-
 dolfin/mesh/Cell.h                                 |    33 +-
 dolfin/mesh/CellType.cpp                           |    46 +-
 dolfin/mesh/CellType.h                             |    17 +-
 dolfin/mesh/DistributedMeshTools.cpp               |     4 +-
 dolfin/mesh/DynamicMeshEditor.cpp                  |     8 +-
 dolfin/mesh/Edge.h                                 |    12 +-
 dolfin/mesh/Face.h                                 |    12 +-
 dolfin/mesh/Facet.h                                |    12 +-
 dolfin/mesh/HexahedronCell.cpp                     |    14 -
 dolfin/mesh/HexahedronCell.h                       |    17 +-
 dolfin/mesh/IntervalCell.cpp                       |    19 +-
 dolfin/mesh/IntervalCell.h                         |    20 +-
 dolfin/mesh/LocalMeshData.cpp                      |     2 +-
 dolfin/mesh/Mesh.cpp                               |     9 +-
 dolfin/mesh/Mesh.h                                 |    27 +-
 dolfin/mesh/MeshColoring.cpp                       |     6 +-
 dolfin/mesh/MeshColoring.h                         |     4 +-
 dolfin/mesh/MeshEditor.cpp                         |    42 +-
 dolfin/mesh/MeshEditor.h                           |    18 -
 dolfin/mesh/MeshFunction.h                         |     8 +-
 dolfin/mesh/MeshHierarchy.cpp                      |    10 +-
 dolfin/mesh/MeshQuality.cpp                        |    10 +-
 dolfin/mesh/MeshQuality.h                          |     4 +-
 dolfin/mesh/MeshRenumbering.cpp                    |     8 +-
 dolfin/mesh/MeshTopology.cpp                       |     5 +-
 dolfin/mesh/MeshTopology.h                         |     4 +-
 dolfin/mesh/MeshTransformation.cpp                 |    18 +-
 dolfin/mesh/MeshTransformation.h                   |    13 +-
 dolfin/mesh/MultiMesh.cpp                          |  1495 ++-
 dolfin/mesh/MultiMesh.h                            |   202 +-
 dolfin/mesh/PointCell.cpp                          |    19 +-
 dolfin/mesh/PointCell.h                            |    19 +-
 dolfin/mesh/QuadrilateralCell.cpp                  |    14 -
 dolfin/mesh/QuadrilateralCell.h                    |    17 +-
 dolfin/mesh/TetrahedronCell.cpp                    |    19 +-
 dolfin/mesh/TetrahedronCell.h                      |    20 +-
 dolfin/mesh/TopologyComputation.cpp                |     4 +-
 dolfin/mesh/TriangleCell.cpp                       |    19 +-
 dolfin/mesh/TriangleCell.h                         |    18 +-
 dolfin/mesh/Vertex.h                               |    12 +-
 dolfin/refinement/BisectionRefinement1D.cpp        |     2 +-
 dolfin/refinement/LocalMeshCoarsening.cpp          |    12 +-
 dolfin/refinement/ParallelRefinement.cpp           |    14 +-
 dolfin/refinement/ParallelRefinement.h             |     8 +-
 dolfin/refinement/RegularCutRefinement.cpp         |     3 +-
 dolfin/refinement/refine.cpp                       |    22 +-
 dolfin/refinement/refine.h                         |     2 +-
 dolfin/swig/la/post.i                              |    13 +-
 dolfin/swig/mesh/post.i                            |    42 +
 dolfin/swig/mesh/pre.i                             |    91 +
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 dolfin/swig/typemaps/std_map.i                     |    27 +
 dolfin/swig/typemaps/std_vector.i                  |    22 +-
 python/CMakeLists.txt                              |    36 +-
 python/cmake/FindPETSc4py.cmake                    |   112 +
 python/doc/Makefile                                |    20 +
 python/doc/source/api.rst                          |    21 +-
 python/dolfin/__init__.py                          |    58 +-
 python/dolfin/common/plotting.py                   |    26 +-
 python/dolfin/common/timer.py                      |     6 +-
 python/dolfin/fem/adaptivesolving.py               |    12 +-
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 python/dolfin/fem/form.py                          |     5 +-
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 python/dolfin/fem/problem.py                       |    95 +
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 python/dolfin/la/solver.py                         |    72 +
 python/dolfin/mesh/__init__.py                     |     3 +
 python/dolfin/mesh/ale.py                          |    38 +-
 python/dolfin/mesh/meshfunction.py                 |    59 +-
 python/dolfin/mesh/subdomain.py                    |    29 +-
 python/dolfin/mesh/svgtools.py                     |    32 +-
 python/dolfin/multistage/__init__.py               |     8 +-
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 python/dolfin/multistage/multistagescheme.py       |   203 +-
 python/dolfin/multistage/multistagesolvers.py      |     1 +
 python/dolfin/multistage/rushlarsenschemes.py      |    74 +-
 python/dolfin/parameter/__init__.py                |    13 +-
 python/dolfin_utils/meshconvert/meshconvert.py     |     2 +-
 python/dolfin_utils/test/fixtures.py               |    80 +-
 python/setup.cfg                                   |     2 +
 python/setup.py                                    |    10 +-
 .../intersect.cpp => python/src/MPICommWrapper.cpp |    32 +-
 .../PETScObject.h => python/src/MPICommWrapper.h   |    45 +-
 python/src/adaptivity.cpp                          |     8 +-
 python/src/ale.cpp                                 |     2 -
 python/src/casters.h                               |     3 +-
 python/src/common.cpp                              |   165 +-
 python/src/dolfin.cpp                              |     4 +-
 python/src/fem.cpp                                 |    46 +-
 python/src/function.cpp                            |    29 +-
 python/src/generation.cpp                          |   101 +-
 python/src/geometry.cpp                            |    31 +-
 python/src/io.cpp                                  |    23 +-
 python/src/la.cpp                                  |   339 +-
 python/src/log.cpp                                 |    23 +-
 python/src/mesh.cpp                                |   112 +-
 python/src/mpi_casters.h                           |   170 +-
 python/src/multistage.cpp                          |     4 +-
 python/src/nls.cpp                                 |    22 +-
 python/src/parameter.cpp                           |    21 +-
 python/src/petsc_casters.h                         |   147 +-
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 test/unit/python/mesh/test_edge.py                 |     2 -
 test/unit/python/mesh/test_face.py                 |     2 -
 .../mesh/{test_mesh_data.py => test_facet.py}      |    26 +-
 test/unit/python/mesh/test_ghost_mesh.py           |     2 -
 .../unit/python/mesh/test_manifold_point_search.py |     7 +-
 test/unit/python/mesh/test_mesh.py                 |   119 +-
 test/unit/python/mesh/test_mesh_coloring.py        |     0
 test/unit/python/mesh/test_mesh_data.py            |     2 -
 test/unit/python/mesh/test_mesh_editor.py          |     2 -
 test/unit/python/mesh/test_mesh_function.py        |    18 +-
 test/unit/python/mesh/test_mesh_iterator.py        |     2 -
 test/unit/python/mesh/test_mesh_markers.py         |     2 -
 test/unit/python/mesh/test_mesh_quality.py         |     2 -
 test/unit/python/mesh/test_mesh_transformation.py  |     2 -
 .../unit/python/mesh/test_mesh_value_collection.py |    10 +-
 .../python/mesh/test_multi_mesh_integration.py     |   113 -
 .../mesh/test_periodic_boundary_computation.py     |     2 -
 test/unit/python/mesh/test_sub_domain.py           |    32 +-
 test/unit/python/mesh/test_sub_mesh.py             |     6 +-
 .../unit/python/meshconvert/test_mesh_converter.py |     8 +-
 test/unit/python/multimesh/test_compression.py     |   103 +
 test/unit/python/multimesh/test_interface_area.py  |   139 +
 test/unit/python/multimesh/test_multimesh.py       |    58 +-
 .../python/multimesh/test_multimesh_cell_types.py  |    94 +
 .../multimesh/test_multimesh_coefficients.py       |   113 +
 .../test_multimesh_initialization.py}              |    41 +-
 .../unit/python/multimesh/test_multimesh_issues.py |    69 +
 test/unit/python/multimesh/test_multimesh_solve.py |   125 +
 test/unit/python/multimesh/test_volume.py          |   206 +
 test/unit/python/multistage/test_RK_solver.py      |     8 +-
 .../multistage/test_point_integral_solver.py       |     2 -
 test/unit/python/nls/test_PETScSNES_solver.py      |     2 -
 test/unit/python/nls/test_PETScTAOSolver.py        |     2 -
 .../python/nls/test_TAO_linear_bound_solver.py     |     2 -
 .../test_solve_result_against_reference.py         |     5 +-
 test/unit/python/parameter/test_parameters.py      |     4 +-
 .../test_assembly_derivatives.py                   |     2 -
 .../ufl-jit-assemble-chain/test_form_operations.py |     2 -
 417 files changed, 32479 insertions(+), 8938 deletions(-)

-- 
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