[dolfin] branch master updated (20847c9 -> 235d3dd)
Johannes Ring
johannr-guest at moszumanska.debian.org
Mon Jul 4 12:13:28 UTC 2016
This is an automated email from the git hooks/post-receive script.
johannr-guest pushed a change to branch master
in repository dolfin.
from 20847c9 upload 1.6.0-5 to unstable
new c0a1581 Imported Upstream version 2016.1.0
new f9129e0 Merge tag 'upstream/2016.1.0'
new 235d3dd Update for 2016.1 release
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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 +-
.../cpp/main.cpp | 3 +
.../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/{FindSphinx.cmake => FindUFC.cmake} | 77 +-
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 +-
debian/changelog | 13 +
debian/control | 20 +-
...ibdolfin1.6.install => libdolfin2016.1.install} | 0
debian/rules | 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 +-
.../stokes-iterative/python/documentation.rst | 22 +-
.../stokes-mini/python/demo_stokes-mini.py | 25 +-
.../stokes-mini/python/documentation.rst | 53 +-
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
.../dolfin_fine_subdomains.xml.gz | Bin 42459 -> 0 bytes
demo/documented/stokes-stabilized/plot_p.png | Bin 49829 -> 0 bytes
demo/documented/stokes-stabilized/plot_u.png | Bin 94743 -> 0 bytes
.../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 | 9 +-
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 +
.../ghost-mesh/python/demo_ghost-mesh.py | 39 +-
.../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 +-
.../lift-drag/python/demo_lift-drag.py | 2 +-
demo/undocumented/mesh-quality/cpp/CMakeLists.txt | 43 +-
demo/undocumented/mesh-quality/python/.gitignore | 1 +
.../mesh-quality/python/demo_mesh-quality.py | 4 +-
.../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 +
.../python/demo_multistage-solver.py | 2 +-
.../nonmatching-interpolation/cpp/CMakeLists.txt | 43 +-
.../nonmatching-interpolation/cpp/P1.h | 376 +-
.../nonmatching-interpolation/cpp/P3.h | 594 +-
.../nonmatching-interpolation/cpp/compile.log | 212 +-
.../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 +-
.../nonmatching-projection/cpp/main.cpp | 14 +-
.../optimization/python/demo_optimization.py | 2 +-
.../parallel-refinement/cpp/CMakeLists.txt | 43 +-
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.cpp | 37 -
.../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.cpp | 53 -
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 +-
.../poisson-disc/cpp/PoissonDisc.ufl} | 40 +-
demo/undocumented/poisson-disc/cpp/compile.log | 2073 ++
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demo/undocumented/waveguide/cpp/main.cpp | 34 +-
{doc => doc-old}/CMakeLists.txt | 0
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{doc => doc-old}/man/man1/dolfin-convert.1.gz | Bin
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dolfin/adaptivity/ErrorControl.cpp | 88 +-
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dolfin/adaptivity/adaptivesolve.cpp | 54 +-
dolfin/adaptivity/dolfin_adaptivity.h | 1 -
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dolfin/ale/ALE.h | 58 +-
dolfin/ale/HarmonicSmoothing.cpp | 27 +-
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dolfin/ale/MeshDisplacement.cpp | 19 +-
dolfin/ale/MeshDisplacement.h | 3 +-
dolfin/ale/Poisson1D.h | 1870 +-
dolfin/ale/Poisson2D.h | 2757 +-
dolfin/ale/Poisson3D.h | 4371 ++-
dolfin/ale/compile.log | 375 +-
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dolfin/common/MPI.h | 34 +-
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dolfin/common/Timer.cpp | 7 -
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dolfin/common/timing.cpp | 5 -
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dolfin/common/unittest.h | 40 -
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dolfin/common/version.h.in | 1 +
dolfin/fem/Assembler.cpp | 54 +-
dolfin/fem/Assembler.h | 10 +-
dolfin/fem/AssemblerBase.cpp | 124 +-
dolfin/fem/BasisFunction.h | 49 +-
dolfin/fem/DirichletBC.cpp | 261 +-
dolfin/fem/DirichletBC.h | 102 +-
dolfin/fem/DiscreteOperators.cpp | 167 +
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dolfin/fem/DofMap.cpp | 221 +-
dolfin/fem/DofMap.h | 119 +-
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dolfin/fem/DomainAssigner.h | 127 -
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dolfin/fem/Form.cpp | 71 +-
dolfin/fem/Form.h | 78 +-
dolfin/fem/GenericDofMap.h | 40 +-
dolfin/fem/LinearTimeDependentProblem.cpp | 71 +-
dolfin/fem/LinearTimeDependentProblem.h | 27 +-
dolfin/fem/LinearVariationalProblem.cpp | 63 +-
dolfin/fem/LinearVariationalProblem.h | 30 +-
dolfin/fem/LinearVariationalSolver.cpp | 42 +-
dolfin/fem/LinearVariationalSolver.h | 6 +-
dolfin/fem/LocalAssembler.cpp | 306 +
dolfin/fem/LocalAssembler.h | 111 +
dolfin/fem/LocalSolver.cpp | 411 +-
dolfin/fem/LocalSolver.h | 53 +-
dolfin/fem/MultiMeshAssembler.cpp | 544 +-
dolfin/fem/MultiMeshDirichletBC.cpp | 249 +-
dolfin/fem/MultiMeshDirichletBC.h | 74 +-
dolfin/fem/MultiMeshDofMap.cpp | 30 +-
dolfin/fem/MultiMeshDofMap.h | 25 +-
dolfin/fem/MultiMeshForm.cpp | 31 +-
dolfin/fem/MultiMeshForm.h | 37 +-
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 +-
dolfin/fem/PointSource.h | 16 +-
dolfin/fem/SparsityPatternBuilder.cpp | 91 +-
dolfin/fem/SparsityPatternBuilder.h | 14 +-
dolfin/fem/SystemAssembler.cpp | 247 +-
dolfin/fem/SystemAssembler.h | 48 +-
dolfin/fem/UFC.cpp | 42 +-
dolfin/fem/UFC.h | 96 +-
dolfin/fem/assemble.cpp | 50 +-
dolfin/fem/assemble.h | 53 +-
dolfin/fem/assemble_local.cpp | 83 +
dolfin/{ale/ALEType.h => fem/assemble_local.h} | 20 +-
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 +-
dolfin/function/Constant.cpp | 44 +
dolfin/function/Constant.h | 17 +-
dolfin/function/Expression.cpp | 9 +-
dolfin/function/Expression.h | 10 +-
dolfin/function/Function.cpp | 214 +-
dolfin/function/Function.h | 59 +-
dolfin/function/FunctionAXPY.cpp | 25 +-
dolfin/function/FunctionAXPY.h | 16 +-
dolfin/function/FunctionAssigner.cpp | 17 +-
dolfin/function/FunctionSpace.cpp | 206 +-
dolfin/function/FunctionSpace.h | 65 +-
dolfin/function/GenericFunction.cpp | 4 +-
dolfin/function/GenericFunction.h | 9 +-
dolfin/function/LagrangeInterpolator.cpp | 42 +-
dolfin/function/LagrangeInterpolator.h | 96 +-
...signer.cpp => MultiMeshCoefficientAssigner.cpp} | 28 +-
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dolfin/function/MultiMeshFunction.cpp | 19 +-
dolfin/function/MultiMeshFunction.h | 18 +-
dolfin/function/MultiMeshFunctionSpace.cpp | 40 +-
dolfin/function/MultiMeshFunctionSpace.h | 40 +-
dolfin/function/MultiMeshSubSpace.cpp | 18 +-
dolfin/function/MultiMeshSubSpace.h | 4 +-
dolfin/function/SpecialFunctions.cpp | 22 +-
dolfin/function/SpecialFunctions.h | 15 +-
dolfin/function/SubSpace.cpp | 62 -
dolfin/function/SubSpace.h | 61 -
dolfin/function/dolfin_function.h | 1 -
dolfin/generation/BoxMesh.cpp | 13 +-
dolfin/generation/IntervalMesh.cpp | 5 +-
dolfin/generation/RectangleMesh.cpp | 6 +-
dolfin/generation/SphericalShellMesh.cpp | 102 +
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dolfin/generation/UnitCubeMesh.h | 2 +-
dolfin/generation/UnitDiscMesh.cpp | 127 +
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dolfin/generation/UnitHexMesh.cpp | 4 +-
dolfin/generation/UnitHexMesh.h | 2 +-
dolfin/generation/UnitIntervalMesh.h | 2 +-
dolfin/generation/UnitQuadMesh.cpp | 3 +-
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 +-
dolfin/graph/Graph.h | 1 -
dolfin/graph/GraphBuilder.cpp | 291 +-
dolfin/graph/GraphBuilder.h | 60 +-
dolfin/graph/GraphOrdering.cpp | 196 -
dolfin/graph/GraphOrdering.h | 99 -
dolfin/graph/ParMETIS.cpp | 380 +-
dolfin/graph/ParMETIS.h | 83 +-
dolfin/graph/SCOTCH.cpp | 192 +-
dolfin/graph/SCOTCH.h | 30 +-
dolfin/graph/ZoltanPartition.cpp | 466 -
dolfin/graph/ZoltanPartition.h | 99 -
dolfin/io/Encoder.h | 13 +-
dolfin/io/File.cpp | 40 +-
dolfin/io/File.h | 10 +-
dolfin/io/GenericFile.cpp | 4 +-
dolfin/io/GenericFile.h | 23 +-
dolfin/io/HDF5File.cpp | 1105 +-
dolfin/io/HDF5File.h | 72 +-
dolfin/io/HDF5Interface.cpp | 59 +-
dolfin/io/HDF5Interface.h | 153 +-
dolfin/io/HDF5Utility.cpp | 30 +-
dolfin/io/RAWFile.cpp | 4 +-
dolfin/io/VTKWriter.cpp | 30 +-
dolfin/io/VTKWriter.h | 18 +-
dolfin/io/X3DFile.cpp | 219 +-
dolfin/io/X3DFile.h | 11 -
dolfin/io/X3DOM.cpp | 1059 +
dolfin/io/X3DOM.h | 322 +
dolfin/io/XDMFFile.cpp | 2189 +-
dolfin/io/XDMFFile.h | 364 +-
dolfin/io/XDMFxml.cpp | 265 +-
dolfin/io/XDMFxml.h | 72 +-
dolfin/io/XMLFile.cpp | 8 +-
dolfin/io/XMLMesh.cpp | 12 +-
dolfin/io/XMLMeshValueCollection.h | 2 +-
dolfin/io/XYZFile.cpp | 4 +-
dolfin/io/dolfin_io.h | 1 +
dolfin/io/pugiconfig.hpp | 5 +-
dolfin/io/pugixml.cpp | 2246 +-
dolfin/io/pugixml.hpp | 56 +-
dolfin/io/xmlutils.cpp | 33 +-
dolfin/io/xmlutils.h | 28 +-
dolfin/la/Amesos2LUSolver.cpp | 234 +
dolfin/la/{EigenLUSolver.h => Amesos2LUSolver.h} | 76 +-
dolfin/la/BelosKrylovSolver.cpp | 131 +-
dolfin/la/BelosKrylovSolver.h | 23 +-
dolfin/la/BlockMatrix.cpp | 2 +-
dolfin/la/BlockVector.h | 2 +-
dolfin/la/CoordinateMatrix.cpp | 6 +-
dolfin/la/DefaultFactory.cpp | 24 +-
dolfin/la/DefaultFactory.h | 11 +-
dolfin/la/EigenFactory.h | 26 +-
dolfin/la/EigenKrylovSolver.cpp | 102 +-
dolfin/la/EigenKrylovSolver.h | 13 +-
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 +
dolfin/la/GenericLinearAlgebraFactory.h | 16 +-
dolfin/la/GenericLinearOperator.h | 2 +-
dolfin/la/GenericLinearSolver.h | 9 -
dolfin/la/GenericMatrix.cpp | 3 +-
dolfin/la/GenericMatrix.h | 6 +-
dolfin/la/GenericPreconditioner.h | 66 -
dolfin/la/GenericSparsityPattern.h | 129 -
dolfin/la/GenericTensor.h | 13 +-
dolfin/la/GenericVector.h | 39 +-
dolfin/la/Ifpack2Preconditioner.cpp | 12 +-
dolfin/la/IndexMap.cpp | 138 +
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 +
dolfin/la/LinearOperator.cpp | 19 +-
dolfin/la/LinearOperator.h | 11 +-
dolfin/la/LinearSolver.cpp | 7 +-
dolfin/la/LinearSolver.h | 19 +-
dolfin/la/MUMPSLUSolver.cpp | 209 -
dolfin/la/MUMPSLUSolver.h | 80 -
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 +-
dolfin/la/PETScKrylovSolver.h | 109 +-
dolfin/la/PETScLUSolver.cpp | 227 +-
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 -
dolfin/la/PETScVector.cpp | 374 +-
dolfin/la/PETScVector.h | 42 +-
dolfin/la/PaStiXLUSolver.cpp | 292 -
dolfin/la/PaStiXLUSolver.h | 69 -
dolfin/la/SLEPcEigenSolver.cpp | 279 +-
dolfin/la/SLEPcEigenSolver.h | 87 +-
dolfin/la/STLFactory.cpp | 28 -
dolfin/la/STLFactory.h | 115 -
dolfin/la/STLFactoryCSC.cpp | 26 -
dolfin/la/STLFactoryCSC.h | 60 -
dolfin/la/STLMatrix.cpp | 470 -
dolfin/la/STLMatrix.h | 410 -
dolfin/la/STLVector.h | 33 -
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 +
.../UnitQuadMesh.h => la/TrilinosParameters.h} | 26 +-
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 +-
dolfin/log/Logger.cpp | 32 +-
dolfin/log/Logger.h | 16 +-
dolfin/log/log.cpp | 14 +-
dolfin/log/log.h | 7 +-
dolfin/math/basic.cpp | 20 +-
dolfin/math/basic.h | 3 +-
dolfin/mesh/BoundaryComputation.cpp | 25 +-
dolfin/mesh/BoundaryComputation.h | 9 +-
dolfin/mesh/Cell.h | 101 +-
dolfin/mesh/CellType.cpp | 138 +-
dolfin/mesh/CellType.h | 26 +-
dolfin/mesh/DistributedMeshTools.cpp | 94 +-
dolfin/mesh/DistributedMeshTools.h | 4 +-
dolfin/mesh/DynamicMeshEditor.cpp | 1 -
dolfin/mesh/Edge.h | 5 -
dolfin/mesh/Face.h | 5 -
dolfin/mesh/Facet.h | 6 -
dolfin/mesh/HexahedronCell.cpp | 12 +-
dolfin/mesh/HexahedronCell.h | 10 +-
dolfin/mesh/IntervalCell.cpp | 45 +-
dolfin/mesh/IntervalCell.h | 12 +-
dolfin/mesh/LocalMeshData.cpp | 215 +-
dolfin/mesh/LocalMeshData.h | 110 +-
dolfin/mesh/LocalMeshValueCollection.h | 13 +-
dolfin/mesh/Mesh.cpp | 69 +-
dolfin/mesh/Mesh.h | 62 +-
dolfin/mesh/MeshColoring.cpp | 39 +-
dolfin/mesh/MeshColoring.h | 26 +-
dolfin/mesh/MeshConnectivity.h | 26 +-
dolfin/mesh/MeshEditor.cpp | 70 +-
dolfin/mesh/MeshEditor.h | 30 +-
dolfin/mesh/MeshEntity.cpp | 2 +-
dolfin/mesh/MeshEntity.h | 10 +-
dolfin/mesh/MeshFunction.h | 206 +-
dolfin/mesh/MeshGeometry.cpp | 107 +-
dolfin/mesh/MeshGeometry.h | 117 +-
dolfin/mesh/MeshHierarchy.cpp | 58 +-
dolfin/mesh/MeshPartitioning.cpp | 831 +-
dolfin/mesh/MeshPartitioning.h | 231 +-
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 +-
dolfin/mesh/PointCell.cpp | 15 +-
dolfin/mesh/PointCell.h | 12 +-
dolfin/mesh/QuadrilateralCell.cpp | 14 +-
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dolfin/mesh/Restriction.cpp | 84 -
dolfin/mesh/Restriction.h | 118 -
dolfin/mesh/SubDomain.cpp | 2 +-
dolfin/mesh/SubMesh.cpp | 6 +-
dolfin/mesh/TetrahedronCell.cpp | 121 +-
dolfin/mesh/TetrahedronCell.h | 18 +-
dolfin/mesh/TopologyComputation.cpp | 384 +-
dolfin/mesh/TopologyComputation.h | 31 +-
dolfin/mesh/TriangleCell.cpp | 61 +-
dolfin/mesh/TriangleCell.h | 10 +-
dolfin/mesh/Vertex.h | 5 -
dolfin/mesh/dolfin_mesh.h | 1 -
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 +-
dolfin/nls/NewtonSolver.h | 6 +-
dolfin/nls/PETScSNESSolver.cpp | 292 +-
dolfin/nls/PETScSNESSolver.h | 38 +-
dolfin/nls/PETScTAOSolver.cpp | 264 +-
dolfin/nls/PETScTAOSolver.h | 44 +-
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 +-
dolfin/plot/VTKPlotter.h | 85 +-
dolfin/plot/VTKWindowOutputStage.cpp | 130 +-
dolfin/plot/VTKWindowOutputStage.h | 24 +-
dolfin/plot/plot.cpp | 35 +-
dolfin/plot/plot.h | 24 +-
dolfin/refinement/BisectionRefinement1D.cpp | 98 +-
dolfin/refinement/BisectionRefinement1D.h | 8 +-
dolfin/refinement/LocalMeshCoarsening.cpp | 16 +-
dolfin/refinement/LocalMeshRefinement.cpp | 75 -
dolfin/refinement/LocalMeshRefinement.h | 49 -
dolfin/refinement/ParallelRefinement.cpp | 45 +-
dolfin/refinement/ParallelRefinement.h | 2 +-
dolfin/refinement/PlazaRefinementND.cpp | 176 +-
dolfin/refinement/PlazaRefinementND.h | 27 +-
dolfin/refinement/RegularCutRefinement.cpp | 41 +-
dolfin/refinement/RegularCutRefinement.h | 3 +-
dolfin/refinement/UniformMeshRefinement.cpp | 109 -
dolfin/refinement/refine.cpp | 103 +-
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rename dolfin/{refinement/UniformMeshRefinement.h => generation/UnitDiscMesh.h} (63%)
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delete mode 100644 dolfin/graph/GraphOrdering.h
delete mode 100644 dolfin/graph/ZoltanPartition.cpp
delete mode 100644 dolfin/graph/ZoltanPartition.h
create mode 100644 dolfin/io/X3DOM.cpp
create mode 100644 dolfin/io/X3DOM.h
create mode 100644 dolfin/la/Amesos2LUSolver.cpp
copy dolfin/la/{EigenLUSolver.h => Amesos2LUSolver.h} (51%)
delete mode 100644 dolfin/la/GenericPreconditioner.h
delete mode 100644 dolfin/la/GenericSparsityPattern.h
create mode 100644 dolfin/la/IndexMap.cpp
create mode 100644 dolfin/la/IndexMap.h
delete mode 100644 dolfin/la/MUMPSLUSolver.cpp
delete mode 100644 dolfin/la/MUMPSLUSolver.h
delete mode 100644 dolfin/la/PaStiXLUSolver.cpp
delete mode 100644 dolfin/la/PaStiXLUSolver.h
delete mode 100644 dolfin/la/STLFactory.cpp
delete mode 100644 dolfin/la/STLFactory.h
delete mode 100644 dolfin/la/STLFactoryCSC.cpp
delete mode 100644 dolfin/la/STLFactoryCSC.h
delete mode 100644 dolfin/la/STLMatrix.cpp
delete mode 100644 dolfin/la/STLMatrix.h
delete mode 100644 dolfin/la/STLVector.h
create mode 100644 dolfin/la/TrilinosParameters.cpp
copy dolfin/{generation/UnitQuadMesh.h => la/TrilinosParameters.h} (63%)
delete mode 100644 dolfin/mesh/Restriction.cpp
delete mode 100644 dolfin/mesh/Restriction.h
delete mode 100644 dolfin/refinement/LocalMeshRefinement.cpp
delete mode 100644 dolfin/refinement/LocalMeshRefinement.h
delete mode 100644 dolfin/refinement/UniformMeshRefinement.cpp
copy dolfin/swig/{plot => graph}/pre.i (79%)
create mode 100644 dolfin/swig/typemaps/std_array.i
create mode 100644 site-packages/dolfin/fem/assembling_local.py
delete mode 100644 site-packages/dolfin/functions/ufc_functionspace.py
delete mode 100644 test/CMakeLists.txt
rename test/codingstyle/{test_coding_style.py => test_coding_style.py.in} (67%)
create mode 100644 test/unit/CMakeLists.txt
delete mode 100644 test/unit/common/cpp/CMakeLists.txt
delete mode 100755 test/unit/common/cpp/test_cpp_common.py
create mode 100644 test/unit/cpp/CMakeLists.txt
rename test/unit/{common/cpp => cpp/common}/SubSystemsManager.cpp (63%)
create mode 100644 test/unit/cpp/function/Expression.cpp
copy demo/undocumented/curl-curl/cpp/CurrentDensity.h => test/unit/cpp/function/Projection.h (52%)
rename test/unit/{function/cpp => cpp/function}/Projection.ufl (100%)
create mode 100644 test/unit/cpp/function/compile.log
create mode 100644 test/unit/cpp/io/XMLMeshData.cpp
create mode 100644 test/unit/cpp/io/XMLMeshValueCollection.cpp
rename test/unit/{io/cpp => cpp/io}/xml_value_collection_ref.xml (100%)
create mode 100644 test/unit/cpp/la/LinearOperator.cpp
create mode 100644 test/unit/cpp/la/Vector.cpp
copy demo/undocumented/elastodynamics/cpp/DG0_eps_xx.h => test/unit/cpp/la/forms/ReactionDiffusion.h (55%)
rename test/unit/{la/cpp => cpp/la}/forms/ReactionDiffusion.ufl (100%)
copy demo/undocumented/elastodynamics/cpp/DG0_eps_xx.h => test/unit/cpp/la/forms/ReactionDiffusionAction.h (53%)
rename test/unit/{la/cpp => cpp/la}/forms/ReactionDiffusionAction.ufl (100%)
rename test/unit/{la/cpp => cpp/la}/forms/compile.log (64%)
create mode 100644 test/unit/cpp/mesh/Mesh.cpp
create mode 100644 test/unit/cpp/mesh/MeshFunction.cpp
create mode 100644 test/unit/cpp/mesh/MeshValueCollection.cpp
create mode 100644 test/unit/cpp/multimesh/MultiMesh.cpp
rename test/unit/{parameter/cpp => cpp/parameter}/Parameters.cpp (70%)
rename test/unit/{io/cpp/test_cpp_io.py => cpp/test_cpp_unit.py} (71%)
delete mode 100644 test/unit/function/cpp/CMakeLists.txt
delete mode 100644 test/unit/function/cpp/Expression.cpp
delete mode 100644 test/unit/function/cpp/Projection.h
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delete mode 100644 test/unit/io/cpp/CMakeLists.txt
delete mode 100644 test/unit/io/cpp/XMLMeshData.cpp
delete mode 100644 test/unit/io/cpp/XMLMeshValueCollection.cpp
delete mode 100644 test/unit/la/cpp/CMakeLists.txt
delete mode 100644 test/unit/la/cpp/LinearOperator.cpp
delete mode 100644 test/unit/la/cpp/Vector.cpp
delete mode 100644 test/unit/la/cpp/forms/ReactionDiffusion.h
delete mode 100644 test/unit/la/cpp/forms/ReactionDiffusionAction.h
delete mode 100755 test/unit/la/cpp/test_cpp_la.py
delete mode 100644 test/unit/mesh/cpp/CMakeLists.txt
delete mode 100644 test/unit/mesh/cpp/Mesh.cpp
delete mode 100644 test/unit/mesh/cpp/MeshFunction.cpp
delete mode 100644 test/unit/mesh/cpp/MeshValueCollection.cpp
delete mode 100755 test/unit/mesh/cpp/test_cpp_mesh.py
delete mode 100644 test/unit/multimesh/cpp/CMakeLists.txt
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delete mode 100644 test/unit/multimesh/cpp/MultiMeshStokes2D.h
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delete mode 100644 test/unit/multimesh/cpp/compile.log
delete mode 100755 test/unit/multimesh/cpp/test_cpp_multimesh.py
delete mode 100644 test/unit/parameter/cpp/CMakeLists.txt
delete mode 100755 test/unit/parameter/cpp/test_cpp_parameter.py
create mode 100755 test/unit/python/fem/test_discrete_operators.py
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create mode 100755 test/unit/python/fem/test_local_assembler.py
create mode 100755 test/unit/python/fem/test_symbolic_geometry_assembly.py
copy test/unit/python/fem/{test_solving.py => test_variational_problem.py} (51%)
create mode 100755 test/unit/python/geometry/test_coordinates.py
create mode 100644 test/unit/python/la/test_tensor_layout.py
create mode 100755 test/unit/python/mesh/test_ghost_mesh.py
mode change 100644 => 100755 test/unit/python/mesh/test_manifold_point_search.py
rename utils/xml/convertall => test/unit/python/mpipipe.sh (53%)
mode change 100644 => 100755
mode change 100644 => 100755 test/unit/python/nls/test_PETScTAOSolver.py
delete mode 100644 utils/gid/DOLFIN.bas
delete mode 100644 utils/matlab/meshindex.m
delete mode 100644 utils/matlab/plotcontroller.m
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delete mode 100644 utils/matlab/xmlmatrix.m
delete mode 100644 utils/matlab/xmlmesh.m
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delete mode 100644 utils/octave/README
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delete mode 100644 utils/octave/pdesurf.m
delete mode 100644 utils/python/README
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delete mode 100755 utils/swig/dolfin-swig
delete mode 100644 utils/system/monitor
delete mode 100755 utils/tetgen/dolfin-tetgen
delete mode 100644 utils/vim/macros
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