[dolfin] 02/03: Merge tag 'upstream/2016.1.0'
Johannes Ring
johannr-guest at moszumanska.debian.org
Mon Jul 4 12:13:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
johannr-guest pushed a commit to branch master
in repository dolfin.
commit f9129e08fffd49ba6978c6650f60be5078a6f7bf
Merge: 20847c9 c0a1581
Author: Johannes Ring <johannr at simula.no>
Date: Mon Jun 27 10:24:03 2016 +0200
Merge tag 'upstream/2016.1.0'
Upstream version 2016.1.0
.gitignore | 137 +
AUTHORS | 2 +-
CMakeLists.txt | 359 +-
ChangeLog | 59 +-
INSTALL | 5 +-
README.rst | 21 +-
bench/bench.py | 4 +-
bench/common/progress/cpp/CMakeLists.txt | 43 +-
bench/common/timing/cpp/CMakeLists.txt | 43 +-
bench/fem/assembly/cpp/CMakeLists.txt | 43 +-
bench/fem/assembly/cpp/forms.h | 41 +-
bench/fem/assembly/cpp/forms/Elasticity3D.h | 1292 +-
bench/fem/assembly/cpp/forms/NSEMomentum3D.h | 4363 ++-
bench/fem/assembly/cpp/forms/Poisson2DP1.h | 2757 +-
bench/fem/assembly/cpp/forms/Poisson2DP2.h | 4636 ++-
bench/fem/assembly/cpp/forms/Poisson2DP3.h | 4540 ++-
bench/fem/assembly/cpp/forms/StabStokes2D.h | 1889 +-
bench/fem/assembly/cpp/forms/THStokes2D.h | 8488 +++--
bench/fem/assembly/cpp/forms/compile.log | 2349 +-
bench/fem/assembly/cpp/main.cpp | 9 +-
bench/fem/convergence/cpp/CMakeLists.txt | 43 +-
bench/fem/convergence/cpp/Poisson2D_1.cpp | 2564 +-
bench/fem/convergence/cpp/Poisson2D_1.h | 1048 +-
bench/fem/convergence/cpp/Poisson2D_2.cpp | 4682 ++-
bench/fem/convergence/cpp/Poisson2D_2.h | 1212 +-
bench/fem/convergence/cpp/Poisson2D_3.cpp | 4848 ++-
bench/fem/convergence/cpp/Poisson2D_3.h | 1212 +-
bench/fem/convergence/cpp/Poisson2D_4.cpp | 7684 ++--
bench/fem/convergence/cpp/Poisson2D_4.h | 1212 +-
bench/fem/convergence/cpp/Poisson2D_5.cpp | 2876 +-
bench/fem/convergence/cpp/Poisson2D_5.h | 1212 +-
bench/fem/convergence/cpp/Poisson3D_1.cpp | 4130 ++-
bench/fem/convergence/cpp/Poisson3D_1.h | 1048 +-
bench/fem/convergence/cpp/Poisson3D_2.cpp | 8493 ++++-
bench/fem/convergence/cpp/Poisson3D_2.h | 1212 +-
bench/fem/convergence/cpp/Poisson3D_3.cpp | 8895 +++--
bench/fem/convergence/cpp/Poisson3D_3.h | 1212 +-
bench/fem/convergence/cpp/Poisson3D_4.cpp | 4853 ++-
bench/fem/convergence/cpp/Poisson3D_4.h | 1212 +-
bench/fem/convergence/cpp/compile.log | 2705 +-
bench/fem/convergence/cpp/main.cpp | 90 +-
bench/fem/multicore/cpp/CMakeLists.txt | 43 +-
bench/fem/multicore/cpp/NavierStokes.h | 2443 +-
bench/fem/multicore/cpp/Poisson.h | 4371 ++-
bench/fem/multicore/cpp/compile.log | 459 +-
bench/fem/multicore/cpp/main.cpp | 12 +-
bench/fem/speedup/cpp/CMakeLists.txt | 43 +-
bench/fem/speedup/cpp/Poisson.h | 4747 ++-
bench/fem/speedup/cpp/assemble-poisson.cpp | 6 +-
bench/fem/speedup/cpp/bench_fem_speedup_cpp | 9 +-
bench/fem/speedup/cpp/compile.log | 205 +-
bench/fem/speedup/cpp/solve-poisson.cpp | 35 +-
bench/function/evaluation/cpp/CMakeLists.txt | 43 +-
bench/function/evaluation/cpp/P1.h | 418 +-
bench/function/evaluation/cpp/compile.log | 76 +-
bench/function/evaluation/cpp/main.cpp | 16 +-
.../python/bench_function_extrapolation_python | 9 +-
.../python/bench_function_interpolation_python | 11 +-
.../bounding_box_tree_build/cpp/CMakeLists.txt | 43 +-
.../geometry/bounding_box_tree_build/cpp/main.cpp | 3 +
.../cpp/CMakeLists.txt | 43 +-
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.../cpp/CMakeLists.txt | 43 +-
.../cpp/main.cpp | 3 +
bench/la/cusp/python/bench_la_cusp_python | 90 -
bench/la/vector/access/cpp/CMakeLists.txt | 43 +-
bench/la/vector/assignment/cpp/CMakeLists.txt | 43 +-
bench/logs/bench.log | 17449 ++++++++-
bench/logs/milestones.log | 14 +-
bench/mesh/iteration/cpp/CMakeLists.txt | 43 +-
bench/mesh/iteration/cpp/main.cpp | 4 +-
bench/mesh/refinement/cpp/CMakeLists.txt | 43 +-
bench/mesh/topology/cpp/CMakeLists.txt | 43 +-
bench/mesh/topology/cpp/main.cpp | 8 +
bench/mesh/unitcube/cpp/CMakeLists.txt | 43 +-
bench/plot.py | 70 +-
cmake/modules/FindPETSc.cmake | 87 +-
cmake/modules/FindPaStiX.cmake | 159 -
cmake/modules/FindSLEPc.cmake | 2 +-
cmake/modules/FindUFC.cmake | 81 +
cmake/modules/ResolveCompilerPaths.cmake | 16 +-
cmake/scripts/copy-test-demo-data | 2 +-
cmake/scripts/download-demo-data | 2 -
cmake/scripts/generate-cmakefiles | 51 +-
cmake/scripts/generate-form-files | 2 +-
cmake/templates/UseDOLFIN.cmake.in | 7 +-
cmake/templates/dolfin.conf.in | 4 +-
demo/README | 58 +
.../auto-adaptive-poisson/cpp/AdaptivePoisson.h | 14160 +++----
.../auto-adaptive-poisson/cpp/CMakeLists.txt | 43 +-
.../auto-adaptive-poisson/cpp/compile.log | 1054 +-
demo/documented/auto-adaptive-poisson/cpp/main.cpp | 39 +-
.../auto-adaptive-poisson/python/documentation.rst | 4 +-
demo/documented/bcs/cpp/CMakeLists.txt | 43 +-
demo/documented/bcs/cpp/Poisson.h | 4747 ++-
demo/documented/bcs/cpp/compile.log | 205 +-
demo/documented/bcs/cpp/main.cpp | 14 +-
demo/documented/bcs/python/documentation.rst | 54 +-
demo/documented/biharmonic/cpp/Biharmonic.h | 8002 ++--
demo/documented/biharmonic/cpp/CMakeLists.txt | 43 +-
demo/documented/biharmonic/cpp/compile.log | 480 +-
demo/documented/biharmonic/cpp/documentation.rst | 12 +-
demo/documented/biharmonic/cpp/main.cpp | 12 +-
.../biharmonic/python/demo_biharmonic.py | 2 +-
.../documented/biharmonic/python/documentation.rst | 2 +-
demo/documented/built-in-meshes/cpp/CMakeLists.txt | 43 +-
.../built-in-meshes/python/documentation.rst | 6 +-
demo/documented/cahn-hilliard/common.txt | 26 +-
demo/documented/cahn-hilliard/cpp/CMakeLists.txt | 43 +-
.../cahn-hilliard/cpp/CahnHilliard2D.cpp | 3229 +-
demo/documented/cahn-hilliard/cpp/CahnHilliard2D.h | 1823 +-
.../cahn-hilliard/cpp/CahnHilliard2D.ufl | 3 +-
.../cahn-hilliard/cpp/CahnHilliard3D.cpp | 5289 ++-
demo/documented/cahn-hilliard/cpp/CahnHilliard3D.h | 1823 +-
.../cahn-hilliard/cpp/CahnHilliard3D.ufl | 3 +-
demo/documented/cahn-hilliard/cpp/compile.log | 5898 ++-
.../documented/cahn-hilliard/cpp/documentation.rst | 85 +-
demo/documented/cahn-hilliard/cpp/main.cpp | 41 +-
.../cahn-hilliard/python/demo_cahn-hilliard.py | 10 +-
.../cahn-hilliard/python/documentation.rst | 19 +-
demo/documented/eigenvalue/cpp/CMakeLists.txt | 43 +-
demo/documented/eigenvalue/cpp/StiffnessMatrix.h | 4371 ++-
demo/documented/eigenvalue/cpp/compile.log | 194 +-
demo/documented/eigenvalue/cpp/main.cpp | 8 +-
demo/documented/hyperelasticity/cpp/CMakeLists.txt | 43 +-
.../hyperelasticity/cpp/HyperElasticity.h | 2992 +-
.../hyperelasticity/cpp/HyperElasticity.ufl | 2 +-
demo/documented/hyperelasticity/cpp/compile.log | 757 +-
.../hyperelasticity/cpp/documentation.rst | 44 +-
demo/documented/hyperelasticity/cpp/main.cpp | 28 +-
.../hyperelasticity/python/demo_hyperelasticity.py | 6 +-
.../hyperelasticity/python/documentation.rst | 6 +-
.../mixed-poisson-dual/cpp/CMakeLists.txt | 43 +-
.../mixed-poisson-dual/cpp/MixedPoissonDual.h | 5078 ++-
demo/documented/mixed-poisson-dual/cpp/compile.log | 577 +-
.../mixed-poisson-dual/cpp/documentation.rst | 16 +-
demo/documented/mixed-poisson-dual/cpp/main.cpp | 15 +-
.../python/demo_mixed-poisson-dual.py | 12 +-
.../mixed-poisson-dual/python/documentation.rst | 30 +-
demo/documented/mixed-poisson/cpp/CMakeLists.txt | 43 +-
demo/documented/mixed-poisson/cpp/MixedPoisson.h | 4228 ++-
demo/documented/mixed-poisson/cpp/compile.log | 295 +-
.../documented/mixed-poisson/cpp/documentation.rst | 15 +-
demo/documented/mixed-poisson/cpp/main.cpp | 13 +-
.../mixed-poisson/python/demo_mixed-poisson.py | 14 +-
.../mixed-poisson/python/documentation.rst | 32 +-
demo/documented/navier-stokes/cpp/CMakeLists.txt | 43 +-
demo/documented/navier-stokes/cpp/PressureUpdate.h | 4538 ++-
.../navier-stokes/cpp/TentativeVelocity.h | 5670 ++-
demo/documented/navier-stokes/cpp/VelocityUpdate.h | 8041 ++--
demo/documented/navier-stokes/cpp/compile.log | 2897 +-
.../documented/navier-stokes/cpp/documentation.rst | 46 +-
demo/documented/navier-stokes/cpp/main.cpp | 44 +-
.../navier-stokes/python/demo_navier-stokes.py | 2 +-
.../navier-stokes/python/documentation.rst | 2 +-
demo/documented/neumann-poisson/cpp/CMakeLists.txt | 43 +-
demo/documented/neumann-poisson/cpp/Poisson.h | 4196 ++-
demo/documented/neumann-poisson/cpp/compile.log | 194 +-
demo/documented/neumann-poisson/cpp/main.cpp | 23 +-
.../neumann-poisson/python/demo_neumann-poisson.py | 14 +-
.../neumann-poisson/python/documentation.rst | 54 +-
.../nonlinear-poisson/cpp/CMakeLists.txt | 43 +-
.../nonlinear-poisson/cpp/NonlinearPoisson.h | 3239 +-
demo/documented/nonlinear-poisson/cpp/compile.log | 147 +-
demo/documented/nonlinear-poisson/cpp/main.cpp | 18 +-
.../python/demo_nonlinear-poisson.py | 5 +-
.../nonlinear-poisson/python/documentation.rst | 51 +-
demo/documented/periodic/cpp/CMakeLists.txt | 43 +-
demo/documented/periodic/cpp/Poisson.h | 3181 +-
demo/documented/periodic/cpp/compile.log | 120 +-
demo/documented/periodic/cpp/main.cpp | 12 +-
demo/documented/periodic/python/demo_periodic.py | 2 +-
demo/documented/periodic/python/documentation.rst | 93 +-
demo/documented/poisson/cpp/CMakeLists.txt | 43 +-
demo/documented/poisson/cpp/Poisson.h | 3283 +-
demo/documented/poisson/cpp/compile.log | 131 +-
demo/documented/poisson/cpp/documentation.rst | 12 +-
demo/documented/poisson/cpp/main.cpp | 12 +-
demo/documented/poisson/python/demo_poisson.py | 4 +-
demo/documented/poisson/python/documentation.rst | 4 +-
.../documented/singular-poisson/cpp/CMakeLists.txt | 43 +-
demo/documented/singular-poisson/cpp/Poisson.h | 3283 +-
demo/documented/singular-poisson/cpp/compile.log | 131 +-
demo/documented/singular-poisson/cpp/main.cpp | 19 +-
.../python/demo_singular-poisson.py | 15 +-
.../singular-poisson/python/documentation.rst | 69 +-
.../documented/stokes-iterative/cpp/CMakeLists.txt | 43 +-
demo/documented/stokes-iterative/cpp/Stokes.h | 16346 ++++----
.../stokes-iterative/cpp/StokesPreconditioner.h | 15960 ++++----
demo/documented/stokes-iterative/cpp/compile.log | 2492 +-
demo/documented/stokes-iterative/cpp/main.cpp | 33 +-
.../python/demo_stokes-iterative.py | 11 +-
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demo/documented/stokes-stabilized/common.txt | 84 -
.../stokes-stabilized/cpp/CMakeLists.txt | 46 -
demo/documented/stokes-stabilized/cpp/Stokes.h | 6299 ----
demo/documented/stokes-stabilized/cpp/Stokes.ufl | 40 -
demo/documented/stokes-stabilized/cpp/compile.log | 953 -
.../stokes-stabilized/cpp/documentation.rst | 6 -
demo/documented/stokes-stabilized/cpp/main.cpp | 116 -
demo/documented/stokes-stabilized/cpp/plot.py | 9 -
.../stokes-stabilized/dolfin_fine.xml.gz | Bin 88283 -> 0 bytes
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demo/documented/stokes-stabilized/plot_p.png | Bin 49829 -> 0 bytes
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.../python/demo_stokes-stabilized.py | 82 -
.../stokes-stabilized/python/documentation.rst | 133 -
.../stokes-taylor-hood/cpp/CMakeLists.txt | 43 +-
demo/documented/stokes-taylor-hood/cpp/Stokes.h | 9180 +++--
demo/documented/stokes-taylor-hood/cpp/compile.log | 538 +-
demo/documented/stokes-taylor-hood/cpp/main.cpp | 24 +-
.../python/demo_stokes-taylor-hood.py | 9 +-
.../stokes-taylor-hood/python/documentation.rst | 112 +-
.../python/demo_subdomains-poisson.py | 4 +-
.../subdomains-poisson/python/documentation.rst | 4 +-
demo/documented/subdomains/cpp/CMakeLists.txt | 43 +-
demo/documented/subdomains/cpp/main.cpp | 8 +-
.../documented/subdomains/python/documentation.rst | 98 +-
.../python/demo_tensor-weighted-poisson.py | 4 +-
.../python/documentation.rst | 172 +-
.../python/demo_adaptive-poisson.py | 4 +-
.../advection-diffusion/cpp/AdvectionDiffusion.h | 4235 ++-
.../advection-diffusion/cpp/CMakeLists.txt | 43 +-
.../advection-diffusion/cpp/Velocity.h | 912 +-
.../advection-diffusion/cpp/compile.log | 595 +-
demo/undocumented/advection-diffusion/cpp/main.cpp | 32 +-
demo/undocumented/ale/cpp/CMakeLists.txt | 43 +-
demo/undocumented/ale/cpp/main.cpp | 19 +-
demo/undocumented/ale/python/demo_ale.py | 2 +-
.../cpp/AdaptiveNavierStokes.h | 37007 ++++++++++---------
.../auto-adaptive-navier-stokes/cpp/CMakeLists.txt | 43 +-
.../auto-adaptive-navier-stokes/cpp/compile.log | 17207 ++++-----
.../auto-adaptive-navier-stokes/cpp/main.cpp | 51 +-
.../python/demo_auto-adaptive-navier-stokes.py | 8 +-
demo/undocumented/block-matrix/cpp/CMakeLists.txt | 43 +-
.../block-matrix/cpp/StiffnessMatrix.h | 3109 +-
demo/undocumented/block-matrix/cpp/compile.log | 131 +-
demo/undocumented/block-matrix/cpp/main.cpp | 4 +-
.../buckling-tao/python/demo_buckling-tao.py | 25 +-
.../python/demo_collision-detection.py | 5 +
demo/undocumented/coloring/cpp/CMakeLists.txt | 43 +-
demo/undocumented/coloring/cpp/main.cpp | 22 +-
.../python/Probe/Probe.cpp | 6 +-
.../compiled-extension-module/python/Probe/Probe.h | 2 +-
.../python/demo_compiled-extension-module.py | 6 +-
demo/undocumented/conditional/cpp/CMakeLists.txt | 43 +-
demo/undocumented/conditional/cpp/Conditional.h | 5235 ++-
demo/undocumented/conditional/cpp/compile.log | 173 +-
demo/undocumented/conditional/cpp/main.cpp | 8 +-
.../contact-vi-snes/cpp/CMakeLists.txt | 43 +-
.../contact-vi-snes/cpp/HyperElasticity.h | 2612 +-
demo/undocumented/contact-vi-snes/cpp/compile.log | 308 +-
demo/undocumented/contact-vi-snes/cpp/main.cpp | 38 +-
.../contact-vi-snes/python/demo_contact-vi-snes.py | 22 +-
.../undocumented/contact-vi-tao/cpp/CMakeLists.txt | 43 +-
demo/undocumented/contact-vi-tao/cpp/Elasticity.h | 2480 +-
demo/undocumented/contact-vi-tao/cpp/compile.log | 194 +-
demo/undocumented/contact-vi-tao/cpp/main.cpp | 20 +-
.../contact-vi-tao/python/demo_contact-vi-tao.py | 22 +-
demo/undocumented/coordinates/cpp/README | 1 +
.../coordinates/python/demo_coordinates.py | 52 +
demo/undocumented/curl-curl/cpp/CMakeLists.txt | 43 +-
demo/undocumented/curl-curl/cpp/CurrentDensity.h | 6688 ++--
demo/undocumented/curl-curl/cpp/EddyCurrents.h | 2178 +-
.../undocumented/curl-curl/cpp/P1Space.h | 436 +-
.../undocumented/curl-curl/cpp/P1Space.ufl | 14 +-
demo/undocumented/curl-curl/cpp/compile.log | 981 +-
demo/undocumented/curl-curl/cpp/main.cpp | 156 +-
.../curl-curl/python/demo_curl-curl.py | 133 +-
.../cpp/AdvectionDiffusion.h | 6276 +++-
.../dg-advection-diffusion/cpp/CMakeLists.txt | 43 +-
.../dg-advection-diffusion/cpp/Projection.h | 3456 +-
.../dg-advection-diffusion/cpp/Velocity.h | 912 +-
.../dg-advection-diffusion/cpp/compile.log | 1600 +-
.../dg-advection-diffusion/cpp/main.cpp | 24 +-
.../python/demo_dg-advection-diffusion.py | 2 +-
demo/undocumented/dg-poisson/cpp/CMakeLists.txt | 43 +-
demo/undocumented/dg-poisson/cpp/Poisson.h | 4558 ++-
demo/undocumented/dg-poisson/cpp/compile.log | 281 +-
demo/undocumented/dg-poisson/cpp/main.cpp | 16 +-
.../dg-poisson/python/demo_dg-poisson.py | 6 +-
demo/undocumented/elasticity/cpp/CMakeLists.txt | 43 +-
demo/undocumented/elasticity/cpp/Elasticity.h | 10045 ++---
demo/undocumented/elasticity/cpp/compile.log | 925 +-
demo/undocumented/elasticity/cpp/main.cpp | 95 +-
.../elasticity/python/demo_elasticity.py | 38 +-
.../undocumented/elastodynamics/cpp/CMakeLists.txt | 43 +-
demo/undocumented/elastodynamics/cpp/DG0_eps_xx.h | 1743 +-
.../elastodynamics/cpp/ElastoDynamics.h | 3213 +-
demo/undocumented/elastodynamics/cpp/compile.log | 349 +-
demo/undocumented/elastodynamics/cpp/main.cpp | 70 +-
.../elastodynamics/python/demo_elastodynamics.py | 10 +-
demo/undocumented/eval/cpp/CMakeLists.txt | 43 +-
demo/undocumented/eval/cpp/Projection.h | 9029 +++--
demo/undocumented/eval/cpp/compile.log | 312 +-
demo/undocumented/eval/cpp/main.cpp | 8 +-
demo/undocumented/eval/python/demo_eval.py | 2 +-
demo/undocumented/extrapolation/cpp/CMakeLists.txt | 43 +-
demo/undocumented/extrapolation/cpp/P1.h | 376 +-
demo/undocumented/extrapolation/cpp/P2.h | 430 +-
demo/undocumented/extrapolation/cpp/compile.log | 164 +-
demo/undocumented/extrapolation/cpp/main.cpp | 6 +-
.../extrapolation/python/demo_extrapolation.py | 2 +-
demo/undocumented/functional/cpp/CMakeLists.txt | 43 +-
demo/undocumented/functional/cpp/EnergyNorm.h | 4547 ++-
demo/undocumented/functional/cpp/compile.log | 214 +-
demo/undocumented/functional/cpp/main.cpp | 8 +-
demo/undocumented/ghost-mesh/python/.gitignore | 1 +
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.../interpolation/python/demo_interpolation.py | 5 +-
demo/undocumented/lift-drag/cpp/CMakeLists.txt | 43 +-
demo/undocumented/lift-drag/cpp/Functionals.h | 2663 +-
demo/undocumented/lift-drag/cpp/Functionals.ufl | 1 +
demo/undocumented/lift-drag/cpp/compile.log | 147 +-
demo/undocumented/lift-drag/cpp/main.cpp | 10 +-
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demo/undocumented/mesh-quality/cpp/CMakeLists.txt | 43 +-
demo/undocumented/mesh-quality/python/.gitignore | 1 +
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.../meshfunction-refinement/cpp/CMakeLists.txt | 43 +-
.../meshfunction-refinement/cpp/main.cpp | 16 +-
.../python/demo_mixed-poisson-sphere.py | 21 +-
demo/undocumented/mplot/cpp/README | 2 +
demo/undocumented/mplot/python/.gitignore | 2 +
demo/undocumented/mplot/python/demo_mplot.py | 132 +
.../multimesh-poisson/cpp/CMakeLists.txt | 43 +-
.../multimesh-poisson/cpp/MultiMeshPoisson.h | 3440 +-
.../multimesh-poisson/cpp/MultiMeshPoisson.ufl | 30 +-
.../undocumented/multimesh-poisson/cpp/compile.log | 184 +-
demo/undocumented/multimesh-poisson/cpp/main.cpp | 133 +-
.../python/demo_multimesh-poisson.py | 132 +
.../multimesh-stokes/cpp/CMakeLists.txt | 43 +-
.../multimesh-stokes/cpp/MultiMeshStokes.h | 10032 ++---
.../multimesh-stokes/cpp/MultiMeshStokes.ufl | 45 +-
demo/undocumented/multimesh-stokes/cpp/Stokes.h | 9180 +++--
demo/undocumented/multimesh-stokes/cpp/compile.log | 1222 +-
demo/undocumented/multimesh-stokes/cpp/main.cpp | 172 +-
.../python/demo_multimesh-stokes.py | 167 +
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.../nonmatching-interpolation/cpp/main.cpp | 8 +-
.../nonmatching-projection/cpp/CMakeLists.txt | 43 +-
.../nonmatching-projection/cpp/P1_projection.h | 7076 ++--
demo/undocumented/nonmatching-projection/cpp/P3.h | 594 +-
.../nonmatching-projection/cpp/compile.log | 389 +-
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.../optimization/python/demo_optimization.py | 2 +-
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demo/undocumented/parallel-refinement/cpp/main.cpp | 14 +-
demo/undocumented/parameters/cpp/CMakeLists.txt | 43 +-
.../parameters/python/demo_parameters.py | 9 -
demo/undocumented/petsc4py/python/demo_petsc4py.py | 102 -
.../plot-qt/cpp/BoundaryMeshFunction.h | 48 -
demo/undocumented/plot-qt/cpp/CMakeLists.txt | 103 -
demo/undocumented/plot-qt/cpp/CoordLabel.cpp | 49 -
demo/undocumented/plot-qt/cpp/CoordLabel.h | 49 -
demo/undocumented/plot-qt/cpp/PlotWidget.h | 57 -
demo/undocumented/plot-qt/cpp/Plotter.cpp | 108 -
demo/undocumented/plot-qt/cpp/Plotter.h | 73 -
demo/undocumented/plot-qt/cpp/main.cpp | 106 -
demo/undocumented/plot/cpp/CMakeLists.txt | 43 +-
.../point-integral/python/demo_point-integral.py | 6 +-
demo/undocumented/poisson-disc/cpp/CMakeLists.txt | 45 +
.../Velocity.h => poisson-disc/cpp/PoissonDisc.h} | 2564 +-
demo/undocumented/poisson-disc/cpp/PoissonDisc.ufl | 53 +
demo/undocumented/poisson-disc/cpp/compile.log | 2073 ++
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dolfin/adaptivity/dolfin_adaptivity.h | 1 -
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dolfin/fem/NonlinearVariationalProblem.cpp | 132 +-
dolfin/fem/NonlinearVariationalProblem.h | 80 +-
dolfin/fem/NonlinearVariationalSolver.cpp | 87 +-
dolfin/fem/NonlinearVariationalSolver.h | 78 +-
dolfin/fem/OpenMpAssembler.cpp | 52 +-
dolfin/fem/OpenMpAssembler.h | 10 +-
dolfin/fem/PointSource.cpp | 22 +-
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dolfin/fem/SparsityPatternBuilder.cpp | 91 +-
dolfin/fem/SparsityPatternBuilder.h | 14 +-
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dolfin/fem/SystemAssembler.h | 48 +-
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dolfin/fem/UFC.h | 96 +-
dolfin/fem/assemble.cpp | 50 +-
dolfin/fem/assemble.h | 53 +-
dolfin/fem/assemble_local.cpp | 83 +
dolfin/{la/STLVector.h => fem/assemble_local.h} | 23 +-
dolfin/fem/dolfin_fem.h | 3 +
dolfin/fem/fem_utils.cpp | 228 +-
dolfin/fem/fem_utils.h | 77 +-
dolfin/fem/solve.cpp | 84 +-
dolfin/function/CoefficientAssigner.cpp | 10 +-
dolfin/function/CoefficientAssigner.h | 6 +-
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dolfin/function/FunctionSpace.h | 65 +-
dolfin/function/GenericFunction.cpp | 4 +-
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dolfin/function/MultiMeshFunctionSpace.cpp | 40 +-
dolfin/function/MultiMeshFunctionSpace.h | 40 +-
dolfin/function/MultiMeshSubSpace.cpp | 18 +-
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dolfin/function/SubSpace.h | 61 -
dolfin/function/dolfin_function.h | 1 -
dolfin/generation/BoxMesh.cpp | 13 +-
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dolfin/generation/RectangleMesh.cpp | 6 +-
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dolfin/generation/UnitCubeMesh.h | 2 +-
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dolfin/generation/UnitQuadMesh.h | 3 +-
dolfin/generation/UnitSquareMesh.h | 2 +-
dolfin/generation/dolfin_generation.h | 2 +
dolfin/geometry/BoundingBoxTree.cpp | 31 +-
dolfin/geometry/BoundingBoxTree.h | 17 +-
dolfin/geometry/CollisionDetection.cpp | 13 +-
dolfin/geometry/GenericBoundingBoxTree.cpp | 106 +-
dolfin/geometry/GenericBoundingBoxTree.h | 20 +-
dolfin/geometry/Point.h | 36 +-
dolfin/graph/CSRGraph.h | 44 +-
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dolfin/graph/ParMETIS.cpp | 380 +-
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dolfin/io/Encoder.h | 13 +-
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dolfin/io/XMLFile.cpp | 8 +-
dolfin/io/XMLMesh.cpp | 12 +-
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dolfin/la/Amesos2LUSolver.cpp | 234 +
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dolfin/la/EigenKrylovSolver.cpp | 102 +-
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dolfin/la/EigenMatrix.cpp | 57 +-
dolfin/la/EigenMatrix.h | 5 +-
dolfin/la/EigenVector.cpp | 23 +-
dolfin/la/EigenVector.h | 25 +-
dolfin/la/GenericLUSolver.h | 6 +
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dolfin/la/GenericLinearOperator.h | 2 +-
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dolfin/la/GenericPreconditioner.h | 66 -
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dolfin/la/GenericVector.h | 39 +-
dolfin/la/Ifpack2Preconditioner.cpp | 12 +-
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dolfin/la/IndexMap.h | 133 +
dolfin/la/KrylovSolver.cpp | 81 +-
dolfin/la/KrylovSolver.h | 18 +-
dolfin/la/LUSolver.cpp | 24 +-
dolfin/la/LUSolver.h | 17 +-
dolfin/la/LinearAlgebraObject.h | 4 +
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dolfin/la/LinearOperator.h | 11 +-
dolfin/la/LinearSolver.cpp | 7 +-
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dolfin/la/Matrix.h | 6 +-
dolfin/la/MueluPreconditioner.cpp | 40 +-
dolfin/la/MueluPreconditioner.h | 3 +
dolfin/la/PETScBaseMatrix.cpp | 85 +-
dolfin/la/PETScBaseMatrix.h | 17 +-
dolfin/la/PETScFactory.cpp | 34 +-
dolfin/la/PETScFactory.h | 13 +-
dolfin/la/PETScKrylovSolver.cpp | 545 +-
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dolfin/la/PETScLUSolver.h | 33 +-
dolfin/la/PETScLinearOperator.cpp | 37 +-
dolfin/la/PETScLinearOperator.h | 6 +-
dolfin/la/PETScMatrix.cpp | 433 +-
dolfin/la/PETScMatrix.h | 27 +-
dolfin/la/PETScOptions.cpp | 4 +
dolfin/la/PETScOptions.h | 11 +-
dolfin/la/PETScPreconditioner.cpp | 118 +-
dolfin/la/PETScPreconditioner.h | 25 +-
dolfin/la/PETScUserPreconditioner.cpp | 4 -
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dolfin/la/SLEPcEigenSolver.cpp | 279 +-
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dolfin/la/Scalar.h | 24 +-
dolfin/la/SparsityPattern.cpp | 405 +-
dolfin/la/SparsityPattern.h | 88 +-
dolfin/la/TensorLayout.cpp | 78 +-
dolfin/la/TensorLayout.h | 59 +-
dolfin/la/TpetraFactory.cpp | 38 +-
dolfin/la/TpetraFactory.h | 17 +-
dolfin/la/TpetraMatrix.cpp | 315 +-
dolfin/la/TpetraMatrix.h | 17 +-
dolfin/la/TpetraVector.cpp | 175 +-
dolfin/la/TpetraVector.h | 10 +-
dolfin/la/TrilinosParameters.cpp | 82 +
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dolfin/la/TrilinosPreconditioner.h | 14 +-
dolfin/la/Vector.h | 8 +-
dolfin/la/VectorSpaceBasis.cpp | 34 +-
dolfin/la/VectorSpaceBasis.h | 21 +-
dolfin/la/dolfin_la.h | 12 +-
dolfin/la/solve.cpp | 23 +-
dolfin/la/test_nullspace.cpp | 2 +-
dolfin/log/LogManager.h | 4 +-
dolfin/log/LogStream.cpp | 9 +-
dolfin/log/LogStream.h | 8 +-
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dolfin/log/Logger.h | 16 +-
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dolfin/log/log.h | 7 +-
dolfin/math/basic.cpp | 20 +-
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dolfin/mesh/BoundaryComputation.cpp | 25 +-
dolfin/mesh/BoundaryComputation.h | 9 +-
dolfin/mesh/Cell.h | 101 +-
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dolfin/mesh/LocalMeshData.cpp | 215 +-
dolfin/mesh/LocalMeshData.h | 110 +-
dolfin/mesh/LocalMeshValueCollection.h | 13 +-
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dolfin/mesh/MeshColoring.cpp | 39 +-
dolfin/mesh/MeshColoring.h | 26 +-
dolfin/mesh/MeshConnectivity.h | 26 +-
dolfin/mesh/MeshEditor.cpp | 70 +-
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dolfin/mesh/MeshFunction.h | 206 +-
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dolfin/mesh/MeshGeometry.h | 117 +-
dolfin/mesh/MeshHierarchy.cpp | 58 +-
dolfin/mesh/MeshPartitioning.cpp | 831 +-
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dolfin/mesh/MeshQuality.cpp | 185 +-
dolfin/mesh/MeshQuality.h | 24 +-
dolfin/mesh/MeshRenumbering.cpp | 4 +-
dolfin/mesh/MeshSmoothing.cpp | 58 +-
dolfin/mesh/MeshTopology.cpp | 8 +-
dolfin/mesh/MeshTopology.h | 14 +-
dolfin/mesh/MeshTransformation.cpp | 74 +-
dolfin/mesh/MeshTransformation.h | 88 +-
dolfin/mesh/MeshValueCollection.h | 60 +-
dolfin/mesh/MultiMesh.cpp | 78 +-
dolfin/mesh/MultiMesh.h | 52 +-
dolfin/mesh/PeriodicBoundaryComputation.cpp | 7 +-
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dolfin/mesh/PointCell.h | 12 +-
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dolfin/multistage/MultiStageScheme.cpp | 30 +-
dolfin/multistage/MultiStageScheme.h | 50 +-
dolfin/multistage/PointIntegralSolver.cpp | 309 +-
dolfin/multistage/PointIntegralSolver.h | 54 +-
dolfin/multistage/RKSolver.cpp | 7 +-
dolfin/multistage/RKSolver.h | 6 +-
dolfin/nls/NewtonSolver.cpp | 27 +-
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dolfin/nls/PETScSNESSolver.cpp | 292 +-
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dolfin/nls/PETScTAOSolver.cpp | 264 +-
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dolfin/nls/TAOLinearBoundSolver.cpp | 358 +-
dolfin/nls/TAOLinearBoundSolver.h | 34 +-
dolfin/parameter/GlobalParameters.h | 17 +-
dolfin/parameter/Parameters.cpp | 17 +-
dolfin/plot/VTKPlotter.cpp | 247 +-
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dolfin/refinement/BisectionRefinement1D.cpp | 98 +-
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dolfin/refinement/PlazaRefinementND.cpp | 176 +-
dolfin/refinement/PlazaRefinementND.h | 27 +-
dolfin/refinement/RegularCutRefinement.cpp | 41 +-
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dolfin/refinement/refine.h | 18 +
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dolfin/swig/common/post.i | 46 +
dolfin/swig/common/pre.i | 100 +-
dolfin/swig/fem/docstrings.i | 721 +-
dolfin/swig/fem/post.i | 40 +-
dolfin/swig/fem/pre.i | 80 +-
dolfin/swig/forwarddeclarations.i | 14 +
dolfin/swig/function/docstrings.i | 211 +-
dolfin/swig/function/post.i | 23 +-
dolfin/swig/function/pre.i | 12 +-
dolfin/swig/generation/docstrings.i | 11 +
dolfin/swig/geometry/docstrings.i | 27 +
dolfin/swig/globalincludes.i | 10 +-
dolfin/swig/graph/docstrings.i | 7 +-
.../swig/graph/pre.i | 33 +-
dolfin/swig/io/docstrings.i | 337 +-
dolfin/swig/io/post.i | 24 +
dolfin/swig/io/pre.i | 2 +
dolfin/swig/la/docstrings.i | 803 +-
dolfin/swig/la/post.i | 25 +
dolfin/swig/la/pre.i | 12 +-
dolfin/swig/log/docstrings.i | 5 +-
dolfin/swig/math/docstrings.i | 3 +-
dolfin/swig/mesh/docstrings.i | 493 +-
dolfin/swig/mesh/post.i | 80 +-
dolfin/swig/mesh/pre.i | 50 +-
dolfin/swig/modules/common/dependencies.txt | 2 +-
dolfin/swig/modules/fem/dependencies.txt | 2 +-
dolfin/swig/modules/fem/module.i | 16 +-
dolfin/swig/modules/function/dependencies.txt | 2 +-
dolfin/swig/modules/function/module.i | 11 -
dolfin/swig/modules/io/dependencies.txt | 2 +-
dolfin/swig/modules/io/module.i | 8 +
dolfin/swig/modules/la/dependencies.txt | 2 +-
dolfin/swig/modules/la/module.i | 22 +-
dolfin/swig/modules/mesh/dependencies.txt | 2 +-
dolfin/swig/modules/mesh/module.i | 18 +-
dolfin/swig/multistage/docstrings.i | 11 +-
dolfin/swig/nls/docstrings.i | 69 +-
dolfin/swig/parameter/post.i | 47 +-
dolfin/swig/plot/docstrings.i | 41 +-
dolfin/swig/plot/pre.i | 10 +-
dolfin/swig/refinement/docstrings.i | 25 +
dolfin/swig/shared_ptr_classes.i | 22 +-
dolfin/swig/typemaps/array.i | 1 +
dolfin/swig/typemaps/includes.i | 1 +
dolfin/swig/typemaps/std_array.i | 109 +
dolfin/swig/typemaps/std_map.i | 3 +
dolfin/swig/typemaps/std_pair.i | 55 +-
dolfin/swig/typemaps/std_vector.i | 16 +-
site-packages/dolfin/__init__.py | 1 +
site-packages/dolfin/common/__init__.py | 1 +
site-packages/dolfin/common/constants.py | 1 +
site-packages/dolfin/common/globalparameters.py.in | 44 +-
site-packages/dolfin/common/math.py | 1 +
site-packages/dolfin/common/memory.py | 1 +
site-packages/dolfin/common/plotting.py | 438 +-
site-packages/dolfin/common/time.py | 1 +
site-packages/dolfin/compilemodules/__init__.py | 1 +
.../dolfin/compilemodules/compilemodule.py | 29 +-
site-packages/dolfin/compilemodules/expressions.py | 3 +-
site-packages/dolfin/compilemodules/jit.py | 95 +-
site-packages/dolfin/compilemodules/subdomains.py | 33 +-
.../dolfin/compilemodules/swigimportinfo.py | 68 +-
site-packages/dolfin/cpp/__init__.py | 2 +
site-packages/dolfin/deprecation.py | 1 +
site-packages/dolfin/fem/__init__.py | 3 +
site-packages/dolfin/fem/adaptivesolving.py | 17 +-
site-packages/dolfin/fem/assembling.py | 172 +-
site-packages/dolfin/fem/assembling_local.py | 76 +
site-packages/dolfin/fem/bcs.py | 66 +-
site-packages/dolfin/fem/errorcontrolgenerator.py | 2 +
site-packages/dolfin/fem/form.py | 87 +-
site-packages/dolfin/fem/formmanipulations.py | 94 +-
site-packages/dolfin/fem/interpolation.py | 16 +-
site-packages/dolfin/fem/norms.py | 32 +-
site-packages/dolfin/fem/projection.py | 51 +-
site-packages/dolfin/fem/solving.py | 79 +-
site-packages/dolfin/functions/__init__.py | 1 +
site-packages/dolfin/functions/constant.py | 36 +-
site-packages/dolfin/functions/expression.py | 365 +-
site-packages/dolfin/functions/function.py | 140 +-
site-packages/dolfin/functions/functionspace.py | 874 +-
site-packages/dolfin/functions/specialfunctions.py | 46 +-
.../dolfin/functions/ufc_functionspace.py | 32 -
site-packages/dolfin/importhandler/__init__.py | 1 +
site-packages/dolfin/mesh/__init__.py | 1 +
site-packages/dolfin/mesh/ale.py | 25 +-
.../dolfin/mesh/boundarysubdomainfinder.py | 1 +
site-packages/dolfin/mesh/meshes.py | 10 +-
site-packages/dolfin/mesh/refinement.py | 1 +
site-packages/dolfin/mesh/svgtools.py | 5 +-
site-packages/dolfin/multistage/__init__.py | 1 +
site-packages/dolfin/multistage/factorize.py | 27 +-
.../dolfin/multistage/multistagescheme.py | 56 +-
.../dolfin/multistage/multistagesolvers.py | 1 +
.../dolfin/multistage/rushlarsenschemes.py | 1 +
site-packages/dolfin_utils/commands.py | 1 +
.../dolfin_utils/cppparser/CppHeaderParser.py | 305 +-
site-packages/dolfin_utils/cppparser/__init__.py | 1 +
site-packages/dolfin_utils/cppparser/utils.py | 1 +
.../dolfin_utils/documentation/__init__.py | 1 +
.../dolfin_utils/documentation/docstringutils.py | 1 +
.../documentation/extractdocumentation.py | 1 +
.../dolfin_utils/documentation/generatecpprst.py | 1 +
.../documentation/generatepythonrst.py | 1 +
.../dolfin_utils/documentation/indextemplates.py | 1 +
site-packages/dolfin_utils/meshconvert/abaqus.py | 1 +
.../dolfin_utils/meshconvert/meshconvert.py | 48 +-
.../dolfin_utils/meshconvert/xml_writer.py | 1 +
site-packages/dolfin_utils/ordereddict.py | 1 +
site-packages/dolfin_utils/pjobs/__init__.py | 1 +
site-packages/dolfin_utils/pjobs/pjobs.py | 3 +-
site-packages/dolfin_utils/pjobs/sge.py | 1 +
site-packages/dolfin_utils/pjobs/slurm.py | 1 +
site-packages/dolfin_utils/pjobs/torque.py | 3 +-
site-packages/dolfin_utils/test/__init__.py | 1 +
site-packages/dolfin_utils/test/fixtures.py | 15 +-
site-packages/dolfin_utils/test/paths.py | 3 +-
site-packages/dolfin_utils/test/skips.py | 3 +-
site-packages/dolfin_utils/test/tests.py | 3 +-
site-packages/fenics/__init__.py | 1 +
test/CMakeLists.txt | 58 -
...est_coding_style.py => test_coding_style.py.in} | 45 +-
test/documentation/verify_demo_code_snippets.py | 5 +
test/regression/test.py | 83 +-
test/unit/CMakeLists.txt | 37 +
test/unit/common/cpp/CMakeLists.txt | 46 -
test/unit/common/cpp/test_cpp_common.py | 3 -
test/unit/cpp/CMakeLists.txt | 90 +
.../cpp => cpp/common}/SubSystemsManager.cpp | 42 +-
test/unit/cpp/function/Expression.cpp | 92 +
.../unit/cpp/function/Projection.h | 8432 +++--
.../{function/cpp => cpp/function}/Projection.ufl | 0
test/unit/cpp/function/compile.log | 260 +
test/unit/cpp/io/XMLMeshData.cpp | 75 +
test/unit/cpp/io/XMLMeshValueCollection.cpp | 53 +
.../cpp => cpp/io}/xml_value_collection_ref.xml | 0
test/unit/cpp/la/LinearOperator.cpp | 126 +
test/unit/cpp/la/Vector.cpp | 182 +
.../unit/cpp/la/forms/ReactionDiffusion.h | 2096 +-
.../{la/cpp => cpp/la}/forms/ReactionDiffusion.ufl | 0
.../unit/cpp/la/forms/ReactionDiffusionAction.h | 1990 +-
.../la}/forms/ReactionDiffusionAction.ufl | 0
test/unit/{la/cpp => cpp/la}/forms/compile.log | 233 +-
test/unit/cpp/mesh/Mesh.cpp | 240 +
test/unit/cpp/mesh/MeshFunction.cpp | 85 +
test/unit/cpp/mesh/MeshValueCollection.cpp | 174 +
test/unit/cpp/multimesh/MultiMesh.cpp | 307 +
.../cpp => cpp/parameter}/Parameters.cpp | 68 +-
.../cpp/test_cpp_io.py => cpp/test_cpp_unit.py} | 2 +-
test/unit/function/cpp/CMakeLists.txt | 46 -
test/unit/function/cpp/Expression.cpp | 108 -
test/unit/function/cpp/Projection.h | 4488 ---
test/unit/function/cpp/compile.log | 236 -
test/unit/function/cpp/test_cpp_function.py | 3 -
test/unit/io/cpp/CMakeLists.txt | 48 -
test/unit/io/cpp/XMLMeshData.cpp | 85 -
test/unit/io/cpp/XMLMeshValueCollection.cpp | 65 -
test/unit/la/cpp/CMakeLists.txt | 48 -
test/unit/la/cpp/LinearOperator.cpp | 135 -
test/unit/la/cpp/Vector.cpp | 199 -
test/unit/la/cpp/forms/ReactionDiffusion.h | 2127 --
test/unit/la/cpp/forms/ReactionDiffusionAction.h | 1689 -
test/unit/la/cpp/test_cpp_la.py | 3 -
test/unit/mesh/cpp/CMakeLists.txt | 50 -
test/unit/mesh/cpp/Mesh.cpp | 322 -
test/unit/mesh/cpp/MeshFunction.cpp | 97 -
test/unit/mesh/cpp/MeshValueCollection.cpp | 187 -
test/unit/mesh/cpp/test_cpp_mesh.py | 3 -
test/unit/multimesh/cpp/CMakeLists.txt | 46 -
test/unit/multimesh/cpp/MultiMesh.cpp | 442 -
test/unit/multimesh/cpp/MultiMeshStokes2D.h | 20923 -----------
test/unit/multimesh/cpp/MultiMeshStokes2D.ufl | 104 -
test/unit/multimesh/cpp/compile.log | 1402 -
test/unit/multimesh/cpp/test_cpp_multimesh.py | 3 -
test/unit/parameter/cpp/CMakeLists.txt | 46 -
test/unit/parameter/cpp/test_cpp_parameter.py | 3 -
test/unit/python/adaptivity/test_error_control.py | 12 +-
test/unit/python/adaptivity/test_time_series.py | 4 +-
test/unit/python/ale/test_harmonic_smoothing.py | 14 +-
test/unit/python/book/README | 8 +-
.../stationary/nonlinear_poisson/alg_newton_np.py | 2 +-
.../stationary/nonlinear_poisson/pde_newton_np.py | 2 +-
.../stationary/nonlinear_poisson/picard_np.py | 2 +-
.../stationary/nonlinear_poisson/vp1_np.py | 6 +-
.../stationary/nonlinear_poisson/vp2_np.py | 5 +-
.../chapter_1_files/stationary/poisson/d1_p2D.py | 2 +-
.../chapter_1_files/stationary/poisson/d2_p2D.py | 2 +-
.../chapter_1_files/stationary/poisson/d3_p2D.py | 2 +-
.../chapter_1_files/stationary/poisson/d4_p2D.py | 2 +-
.../chapter_1_files/stationary/poisson/d5_p2D.py | 2 +-
.../chapter_1_files/stationary/poisson/d6_p2D.py | 6 +-
.../chapter_1_files/stationary/poisson/dn1_p2D.py | 4 +-
.../chapter_1_files/stationary/poisson/dn2_p2D.py | 8 +-
.../chapter_1_files/stationary/poisson/dn3_p2D.py | 8 +-
.../chapter_1_files/stationary/poisson/dn4_p2D.py | 8 +-
.../chapter_1_files/stationary/poisson/dnr_p2D.py | 10 +-
.../chapter_1_files/stationary/poisson/mat2_p2D.py | 2 +-
.../stationary/poisson/membrane1.py | 4 +-
.../stationary/poisson/membrane1v.py | 2 +-
.../book/chapter_1_files/stationary/poisson/paD.py | 2 +-
.../chapter_1_files/stationary/poisson/vcp2D.py | 6 +-
.../chapter_1_files/transient/diffusion/d1_d2D.py | 2 +-
.../chapter_1_files/transient/diffusion/d2_d2D.py | 4 +-
.../chapter_1_files/transient/diffusion/sin_daD.py | 13 +-
test/unit/python/book/test_chapter_10.py | 62 +-
test/unit/python/fem/test_assembler.py | 177 +-
test/unit/python/fem/test_dirichlet_bc.py | 8 +-
test/unit/python/fem/test_discrete_operators.py | 64 +
test/unit/python/fem/test_dofmap.py | 212 +-
test/unit/python/fem/test_dp_assemble.py | 41 +-
test/unit/python/fem/test_finite_element.py | 53 +-
test/unit/python/fem/test_form.py | 166 +-
.../fem/test_interior_facet_integral_sides.py | 6 +-
test/unit/python/fem/test_local_assembler.py | 159 +
test/unit/python/fem/test_local_solver.py | 63 +-
test/unit/python/fem/test_manifolds.py | 56 +-
.../python/fem/test_symbolic_geometry_assembly.py | 873 +
test/unit/python/fem/test_system_assembler.py | 75 +-
test/unit/python/fem/test_variational_problem.py | 73 +
test/unit/python/function/test_constant.py | 57 +-
.../function/test_constrained_function_space.py | 39 +-
test/unit/python/function/test_expression.py | 278 +-
test/unit/python/function/test_function.py | 213 +-
.../unit/python/function/test_function_assigner.py | 23 +-
test/unit/python/function/test_function_space.py | 30 +-
.../python/function/test_lagrange_interpolator.py | 9 +-
.../function/test_nonmatching_interpolation.py | 7 +-
.../unit/python/geometry/test_bounding_box_tree.py | 33 +-
test/unit/python/geometry/test_coordinates.py | 125 +
test/unit/python/geometry/test_issues.py | 2 +-
test/unit/python/io/test_HDF5.py | 2 +-
test/unit/python/io/test_HDF5_series.py | 3 +-
test/unit/python/io/test_SVG.py | 9 +
test/unit/python/io/test_X3D.py | 58 +
test/unit/python/io/test_XDMF.py | 346 +-
test/unit/python/io/test_XDMF_cell_output.py | 6 +-
test/unit/python/io/test_XMLFunction.py | 2 +-
test/unit/python/jit/test_jit.py | 25 +-
test/unit/python/la/test_krylov_solver.py | 125 +-
test/unit/python/la/test_la_basic.py | 12 +-
test/unit/python/la/test_linear_operator.py | 1 +
test/unit/python/la/test_matrix.py | 38 +-
test/unit/python/la/test_nullspace.py | 61 +-
test/unit/python/la/test_petsc.py | 83 +-
test/unit/python/la/test_scalar.py | 2 +
test/unit/python/la/test_tensor_layout.py | 114 +
test/unit/python/la/test_vector.py | 11 +-
test/unit/python/math/test_math.py | 18 +
test/unit/python/mesh/test_boundary_mesh.py | 4 +-
test/unit/python/mesh/test_cell.py | 6 +-
test/unit/python/mesh/test_edge.py | 4 +
test/unit/python/mesh/test_face.py | 2 +
test/unit/python/mesh/test_ghost_mesh.py | 100 +
.../unit/python/mesh/test_manifold_point_search.py | 13 +-
test/unit/python/mesh/test_mesh.py | 98 +-
test/unit/python/mesh/test_mesh_coloring.py | 3 +-
test/unit/python/mesh/test_mesh_data.py | 6 +-
test/unit/python/mesh/test_mesh_editor.py | 3 +-
test/unit/python/mesh/test_mesh_function.py | 28 +-
test/unit/python/mesh/test_mesh_markers.py | 4 +
test/unit/python/mesh/test_mesh_quality.py | 19 +-
test/unit/python/mesh/test_mesh_transformation.py | 26 +-
.../unit/python/mesh/test_mesh_value_collection.py | 19 +-
.../python/mesh/test_multi_mesh_integration.py | 27 +-
.../mesh/test_periodic_boundary_computation.py | 6 +-
test/unit/python/mesh/test_sub_domain.py | 53 +-
test/unit/python/mesh/test_sub_mesh.py | 30 +-
.../unit/python/meshconvert/test_mesh_converter.py | 20 +-
.../xml/convertall => test/unit/python/mpipipe.sh | 40 +-
test/unit/python/multistage/test_RK_solver.py | 4 +-
.../multistage/test_point_integral_solver.py | 16 +-
test/unit/python/nls/test_PETScSNES_solver.py | 14 +-
test/unit/python/nls/test_PETScTAOSolver.py | 2 +-
.../python/nls/test_TAO_linear_bound_solver.py | 2 +-
.../test_solve_result_against_reference.py | 7 +
test/unit/python/parameter/test_parameters.py | 9 +-
utils/gid/DOLFIN.bas | 17 -
utils/matlab/meshindex.m | 54 -
utils/matlab/plotcontroller.m | 35 -
utils/matlab/plotslab.m | 173 -
utils/matlab/xmlmatrix.m | 72 -
utils/matlab/xmlmesh.m | 97 -
utils/matlab/xmlvector.m | 58 -
utils/octave/README | 28 -
utils/octave/pdemesh.m | 29 -
utils/octave/pdeplot.m | 230 -
utils/octave/pdesurf.m | 26 -
utils/python/README | 2 -
utils/python/extract2d | 88 -
utils/swig/dolfin-swig | 156 -
utils/system/monitor | 42 -
utils/tetgen/dolfin-tetgen | 36 -
utils/vim/macros | 6 -
1121 files changed, 346197 insertions(+), 240850 deletions(-)
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