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Viewing changes to src/demo/ode/courtemanche/plot.py

Committer: Johannes Ring
Date: 2008-03-05 22:43:06 UTC
Revision ID: johannr@simula.no-20080305224306-2npsdyhfdpl2esji

The BIG commit!

files added:
SConstruct

bench

bench/README

bench/bench

bench/fem

bench/fem/assembly

bench/fem/assembly/Advection.form

bench/fem/assembly/Advection.h

bench/fem/assembly/bench.log

bench/fem/assembly/bench.py

bench/fem/assembly/main.cpp

bench/fem/convergence

bench/fem/convergence/Poisson2D_1.form

bench/fem/convergence/Poisson2D_1.h

bench/fem/convergence/Poisson2D_2.form

bench/fem/convergence/Poisson2D_2.h

bench/fem/convergence/Poisson2D_3.form

bench/fem/convergence/Poisson2D_3.h

bench/fem/convergence/Poisson2D_4.form

bench/fem/convergence/Poisson2D_4.h

bench/fem/convergence/Poisson2D_5.form

bench/fem/convergence/Poisson2D_5.h

bench/fem/convergence/Poisson3D_1.form

bench/fem/convergence/Poisson3D_1.h

bench/fem/convergence/Poisson3D_2.form

bench/fem/convergence/Poisson3D_2.h

bench/fem/convergence/Poisson3D_3.form

bench/fem/convergence/Poisson3D_3.h

bench/fem/convergence/Poisson3D_4.form

bench/fem/convergence/Poisson3D_4.h

bench/fem/convergence/Poisson3D_5.form

bench/fem/convergence/Poisson3D_5.h

bench/fem/convergence/README

bench/fem/convergence/bench.log

bench/fem/convergence/bench.py

bench/fem/convergence/main.cpp

bench/fem/passembly

bench/fem/passembly/Nonlinear2D.form

bench/fem/passembly/Nonlinear2D.h

bench/fem/passembly/Poisson.form

bench/fem/passembly/Poisson.h

bench/fem/passembly/Poisson2D.h

bench/fem/passembly/Poisson3D_1.form

bench/fem/passembly/Poisson3D_1.h

bench/fem/passembly/assemble.h

bench/fem/passembly/getopts.cpp

bench/fem/passembly/getopts.h

bench/fem/passembly/main.cpp

bench/fem/passembly/parallel_poisson_cube.sh

bench/fem/passembly/plot.py

bench/fem/passembly/plot_parallel_assembly_time.sh

bench/fem/passembly/sequential_poisson_cube.sh

bench/la

bench/la/bench.log

bench/la/bench.py

bench/la/sparse-matrix

bench/la/sparse-matrix/Poisson.form.old

bench/la/sparse-matrix/Poisson.h

bench/la/sparse-matrix/VectorPoisson.form.old

bench/la/sparse-matrix/VectorPoisson.h

bench/la/sparse-matrix/main.cpp

bench/la/vector

bench/la/vector/main.cpp

bench/mesh

bench/mesh/bench.log

bench/mesh/bench.py

bench/mesh/main.cpp

bench/ode

bench/ode/reaction

bench/ode/reaction/README

bench/ode/reaction/bench-domain.log

bench/ode/reaction/bench-domain.py

bench/ode/reaction/bench-overhead.log

bench/ode/reaction/bench-overhead.py

bench/ode/reaction/bench-plot.py

bench/ode/reaction/bench-tol.log

bench/ode/reaction/bench-tol.py

bench/ode/reaction/bench.log

bench/ode/reaction/bench.py

bench/ode/reaction/benchutil.py

bench/ode/reaction/checkerror.py

bench/ode/reaction/main.cpp

bench/ode/reaction/parameters-bench.xml

bench/ode/reaction/parameters-plot.xml

bench/ode/reaction/parameters-reference.xml

bench/ode/reaction/reference_1000.data

bench/ode/reaction/reference_16000.data

bench/ode/reaction/reference_2000.data

bench/ode/reaction/reference_4000.data

bench/ode/reaction/reference_8000.data

bench/ode/wave

bench/ode/wave/bench.log

bench/ode/wave/bench.py

bench/ode/wave/main.cpp

bench/ode/wave/parameters-bench.xml

bench/ode/wave/slit.xml.gz

data/SConscript

demo

demo/SConscript

demo/fem

demo/fem/assembly

demo/fem/assembly/cpp

demo/fem/assembly/cpp/ReactionDiffusion.form

demo/fem/assembly/cpp/ReactionDiffusion.h

demo/fem/assembly/cpp/main.cpp

demo/fem/assembly/python

demo/fem/assembly/python/README

demo/fem/simple

demo/fem/simple/cpp

demo/fem/simple/cpp/main.cpp

demo/fem/simple/python

demo/fem/simple/python/demo.py

demo/fem/simple/tetrahedron.xml.gz

demo/la

demo/la/eigensolver

demo/la/eigensolver/cpp

demo/la/eigensolver/cpp/main.cpp

demo/la/eigensolver/python

demo/la/eigensolver/python/demo.py

demo/mesh

demo/mesh/meshfunction

demo/mesh/meshfunction/cpp

demo/mesh/meshfunction/cpp/main.cpp

demo/mesh/meshfunction/cpp/plot.py

demo/mesh/meshfunction/mesh2D.xml.gz

demo/mesh/meshfunction/meshfunction.xml

demo/mesh/meshfunction/python

demo/mesh/meshfunction/python/demo.py

demo/mesh/partitioning

demo/mesh/partitioning/cpp

demo/mesh/partitioning/cpp/main.cpp

demo/mesh/partitioning/python

demo/mesh/partitioning/python/demo.py

demo/mesh/refinement

demo/mesh/refinement/cpp

demo/mesh/refinement/cpp/main.cpp

demo/mesh/refinement/python

demo/mesh/refinement/python/demo.py

demo/mesh/subdomains

demo/mesh/subdomains/cpp

demo/mesh/subdomains/cpp/main.cpp

demo/mesh/subdomains/python

demo/mesh/subdomains/python/demo.py

demo/nls

demo/nls/cahn-hilliard

demo/nls/cahn-hilliard/cpp

demo/nls/cahn-hilliard/cpp/CahnHilliard2D.form

demo/nls/cahn-hilliard/cpp/CahnHilliard2D.h

demo/nls/cahn-hilliard/cpp/CahnHilliard3D.form

demo/nls/cahn-hilliard/cpp/CahnHilliard3D.h

demo/nls/cahn-hilliard/cpp/main.cpp

demo/nls/cahn-hilliard/python

demo/nls/cahn-hilliard/python/README

demo/nls/nonlinearpoisson

demo/nls/nonlinearpoisson/cpp

demo/nls/nonlinearpoisson/cpp/NonlinearPoisson.form

demo/nls/nonlinearpoisson/cpp/NonlinearPoisson.h

demo/nls/nonlinearpoisson/cpp/main.cpp

demo/nls/nonlinearpoisson/python

demo/nls/nonlinearpoisson/python/demo.py

demo/ode

demo/ode/aliev-panfilov

demo/ode/aliev-panfilov/cpp

demo/ode/aliev-panfilov/cpp/main.cpp

demo/ode/aliev-panfilov/cpp/plot.py

demo/ode/aliev-panfilov/python

demo/ode/aliev-panfilov/python/demo.py

demo/ode/complex

demo/ode/complex/main.cpp

demo/ode/complex/plot.py

demo/ode/courtemanche

demo/ode/courtemanche/main.cpp

demo/ode/courtemanche/plot.py

demo/ode/harmonic

demo/ode/harmonic/main.cpp

demo/ode/harmonic/plot.py

demo/ode/homotopy

demo/ode/homotopy/economy

demo/ode/homotopy/economy/CES.h

demo/ode/homotopy/economy/EavesSchmedders.h

demo/ode/homotopy/economy/Economy.h

demo/ode/homotopy/economy/Leontief.h

demo/ode/homotopy/economy/Polemarchakis.h

demo/ode/homotopy/economy/ces.cpp

demo/ode/homotopy/economy/run-tests.sh

demo/ode/homotopy/economy/test.cpp

demo/ode/homotopy/simple

demo/ode/homotopy/simple/main.cpp

demo/ode/homotopy/simple/plot.py

demo/ode/lorenz

demo/ode/lorenz/main.cpp

demo/ode/lorenz/plot.py

demo/ode/method-weights

demo/ode/method-weights/main.cpp

demo/ode/stiff

demo/ode/stiff/TestProblem1.h

demo/ode/stiff/TestProblem2.h

demo/ode/stiff/TestProblem3.h

demo/ode/stiff/TestProblem4.h

demo/ode/stiff/TestProblem5.h

demo/ode/stiff/TestProblem6.h

demo/ode/stiff/TestProblem7.h

demo/ode/stiff/TestProblem8.h

demo/ode/stiff/TestProblem9.h

demo/ode/stiff/main.cpp

demo/ode/stiff/plot.py

demo/ode/stiff/run-tests.sh

demo/pde

demo/pde/convection-diffusion

demo/pde/convection-diffusion/cpp

demo/pde/convection-diffusion/cpp/ConvectionDiffusion.form

demo/pde/convection-diffusion/cpp/ConvectionDiffusion.h

demo/pde/convection-diffusion/cpp/main.cpp

demo/pde/convection-diffusion/python

demo/pde/convection-diffusion/python/demo.py

demo/pde/convection-diffusion/subdomains.xml.gz

demo/pde/convection-diffusion/velocity.xml.gz

demo/pde/dg

demo/pde/dg/cpp

demo/pde/dg/cpp/Poisson.form

demo/pde/dg/cpp/Poisson.h

demo/pde/dg/cpp/main.cpp

demo/pde/dg/cpp/plot.py

demo/pde/dg/python

demo/pde/dg/python/demo.py

demo/pde/dielectric

demo/pde/dielectric/cpp

demo/pde/dielectric/cpp/README

demo/pde/dielectric/python

demo/pde/dielectric/python/demo.py

demo/pde/elasticity

demo/pde/elasticity/cpp

demo/pde/elasticity/cpp/Elasticity.form

demo/pde/elasticity/cpp/Elasticity.h

demo/pde/elasticity/cpp/main.cpp

demo/pde/elasticity/cpp/plot.py

demo/pde/elasticity/python

demo/pde/elasticity/python/demo.py

demo/pde/functional

demo/pde/functional/cpp

demo/pde/functional/cpp/EnergyNorm.form

demo/pde/functional/cpp/EnergyNorm.h

demo/pde/functional/cpp/main.cpp

demo/pde/functional/python

demo/pde/functional/python/demo.py

demo/pde/lift-drag

demo/pde/lift-drag/cpp

demo/pde/lift-drag/cpp/Drag.form

demo/pde/lift-drag/cpp/Drag.h

demo/pde/lift-drag/cpp/Lift.form

demo/pde/lift-drag/cpp/Lift.h

demo/pde/lift-drag/cpp/main.cpp

demo/pde/lift-drag/pressure.xml.gz

demo/pde/lift-drag/python

demo/pde/lift-drag/python/demo.py

demo/pde/mixed-poisson

demo/pde/mixed-poisson/cpp

demo/pde/mixed-poisson/cpp/MixedPoisson.form

demo/pde/mixed-poisson/cpp/MixedPoisson.h

demo/pde/mixed-poisson/cpp/main.cpp

demo/pde/mixed-poisson/cpp/plot.py

demo/pde/mixed-poisson/python

demo/pde/mixed-poisson/python/demo.py

demo/pde/nonlinear-poisson

demo/pde/nonlinear-poisson/cpp

demo/pde/nonlinear-poisson/cpp/NonlinearPoisson.form

demo/pde/nonlinear-poisson/cpp/NonlinearPoisson.h

demo/pde/nonlinear-poisson/cpp/NonlinearPoisson.py

demo/pde/nonlinear-poisson/cpp/main.cpp

demo/pde/nonlinear-poisson/cpp/plot.py

demo/pde/nonlinear-poisson/python

demo/pde/nonlinear-poisson/python/demo.py

demo/pde/periodic

demo/pde/periodic/cpp

demo/pde/periodic/cpp/Poisson.form

demo/pde/periodic/cpp/Poisson.h

demo/pde/periodic/cpp/main.cpp

demo/pde/periodic/python

demo/pde/periodic/python/demo.py

demo/pde/poisson

demo/pde/poisson/cpp

demo/pde/poisson/cpp/Poisson.form

demo/pde/poisson/cpp/Poisson.h

demo/pde/poisson/cpp/README

demo/pde/poisson/cpp/main.cpp

demo/pde/poisson/python

demo/pde/poisson/python/demo.py

demo/pde/poisson1D

demo/pde/poisson1D/cpp

demo/pde/poisson1D/cpp/Poisson.form

demo/pde/poisson1D/cpp/Poisson.h

demo/pde/poisson1D/cpp/main.cpp

demo/pde/poisson1D/python

demo/pde/poisson1D/python/demo.py

demo/pde/stokes

demo/pde/stokes/stabilized

demo/pde/stokes/stabilized/cpp

demo/pde/stokes/stabilized/cpp/Stokes.form

demo/pde/stokes/stabilized/cpp/Stokes.h

demo/pde/stokes/stabilized/cpp/main.cpp

demo/pde/stokes/stabilized/cpp/plot.py

demo/pde/stokes/stabilized/python

demo/pde/stokes/stabilized/python/demo.py

demo/pde/stokes/stabilized/subdomains.xml.gz

demo/pde/stokes/taylor-hood

demo/pde/stokes/taylor-hood/cpp

demo/pde/stokes/taylor-hood/cpp/Stokes.form

demo/pde/stokes/taylor-hood/cpp/Stokes.h

demo/pde/stokes/taylor-hood/cpp/main.cpp

demo/pde/stokes/taylor-hood/cpp/plot.py

demo/pde/stokes/taylor-hood/python

demo/pde/stokes/taylor-hood/python/demo.py

demo/pde/stokes/taylor-hood/subdomains.xml.gz

demo/plot

demo/plot/cpp

demo/plot/cpp/dolfin-2.xml.gz

demo/plot/cpp/main.cpp

demo/plot/python

demo/plot/python/demo.py

demo/plot/python/dolfin-2.xml.gz

demo/quadrature

demo/quadrature/cpp

demo/quadrature/cpp/main.cpp

demo/quadrature/python

demo/quadrature/python/demo.py

doc/SConscript

dolfin

dolfin/SConscript

dolfin/common

dolfin/common/Array.h

dolfin/common/List.h

dolfin/common/TimeDependent.cpp

dolfin/common/TimeDependent.h

dolfin/common/Variable.cpp

dolfin/common/Variable.h

dolfin/common/dolfin_common.h

dolfin/common/simple_array.h

dolfin/common/timing.cpp

dolfin/common/timing.h

dolfin/common/unittest.h

dolfin/common/utils.cpp

dolfin/common/utils.h

dolfin/dolfin.pc.in

dolfin/elements

dolfin/elements/ElementLibrary.cpp

dolfin/elements/ElementLibrary.h

dolfin/elements/dolfin_elements.h

dolfin/elements/elements.py

dolfin/elements/ffc_00.h

dolfin/elements/ffc_01.h

dolfin/elements/ffc_02.h

dolfin/elements/ffc_03.h

dolfin/elements/ffc_04.h

dolfin/elements/ffc_05.h

dolfin/elements/ffc_06.h

dolfin/elements/ffc_07.h

dolfin/elements/ffc_08.h

dolfin/elements/ffc_09.h

dolfin/elements/ffc_10.h

dolfin/elements/ffc_11.h

dolfin/elements/ffc_12.h

dolfin/elements/ffc_13.h

dolfin/elements/ffc_14.h

dolfin/elements/ffc_15.h

dolfin/elements/ffc_16.h

dolfin/elements/ffc_17.h

dolfin/elements/ffc_18.h

dolfin/elements/ffc_19.h

dolfin/elements/ffc_20.h

dolfin/elements/ffc_21.h

dolfin/elements/ffc_22.h

dolfin/elements/ffc_23.h

dolfin/elements/ffc_24.h

dolfin/elements/ffc_25.h

dolfin/elements/ffc_26.h

dolfin/elements/generate.py

dolfin/fem

dolfin/fem/Assembler.cpp

dolfin/fem/Assembler.h

dolfin/fem/BoundaryCondition.cpp

dolfin/fem/BoundaryCondition.h

dolfin/fem/DirichletBC.cpp

dolfin/fem/DirichletBC.h

dolfin/fem/DofMap.cpp

dolfin/fem/DofMap.h

dolfin/fem/DofMapSet.cpp

dolfin/fem/DofMapSet.h

dolfin/fem/Form.cpp

dolfin/fem/Form.h

dolfin/fem/PeriodicBC.cpp

dolfin/fem/PeriodicBC.h

dolfin/fem/SparsityPatternBuilder.cpp

dolfin/fem/SparsityPatternBuilder.h

dolfin/fem/SubSystem.cpp

dolfin/fem/SubSystem.h

dolfin/fem/UFC.cpp

dolfin/fem/UFC.h

dolfin/fem/UFCCell.h

dolfin/fem/UFCMesh.h

dolfin/fem/assemble.cpp

dolfin/fem/assemble.h

dolfin/fem/dolfin_fem.h

dolfin/fem/pAssembler.cpp

dolfin/fem/pAssembler.h

dolfin/function

dolfin/function/ConstantFunction.cpp

dolfin/function/ConstantFunction.h

dolfin/function/DiscreteFunction.cpp

dolfin/function/DiscreteFunction.h

dolfin/function/Function.cpp

dolfin/function/Function.h

dolfin/function/GenericFunction.h

dolfin/function/SpecialFunctions.h

dolfin/function/SubFunction.h

dolfin/function/UserFunction.cpp

dolfin/function/UserFunction.h

dolfin/function/dolfin_function.h

dolfin/graph

dolfin/graph/DirectedClique.cpp

dolfin/graph/DirectedClique.h

dolfin/graph/Graph.cpp

dolfin/graph/Graph.h

dolfin/graph/GraphEditor.cpp

dolfin/graph/GraphEditor.h

dolfin/graph/GraphPartition.cpp

dolfin/graph/GraphPartition.h

dolfin/graph/UndirectedClique.cpp

dolfin/graph/UndirectedClique.h

dolfin/graph/dolfin_graph.h

dolfin/io

dolfin/io/File.cpp

dolfin/io/File.h

dolfin/io/GenericFile.cpp

dolfin/io/GenericFile.h

dolfin/io/MFile.cpp

dolfin/io/MFile.h

dolfin/io/MatlabFile.cpp

dolfin/io/MatlabFile.h

dolfin/io/OctaveFile.cpp

dolfin/io/OctaveFile.h

dolfin/io/OpenDXFile.cpp

dolfin/io/OpenDXFile.h

dolfin/io/PythonFile.cpp

dolfin/io/PythonFile.h

dolfin/io/VTKFile.cpp

dolfin/io/VTKFile.h

dolfin/io/XMLBLASFormData.cpp

dolfin/io/XMLBLASFormData.h

dolfin/io/XMLDofMap.cpp

dolfin/io/XMLDofMap.h

dolfin/io/XMLFile.cpp

dolfin/io/XMLFile.h

dolfin/io/XMLFiniteElement.cpp

dolfin/io/XMLFiniteElement.h

dolfin/io/XMLFunction.cpp

dolfin/io/XMLFunction.h

dolfin/io/XMLGraph.cpp

dolfin/io/XMLGraph.h

dolfin/io/XMLMatrix.cpp

dolfin/io/XMLMatrix.h

dolfin/io/XMLMesh.cpp

dolfin/io/XMLMesh.h

dolfin/io/XMLMeshFunction.cpp

dolfin/io/XMLMeshFunction.h

dolfin/io/XMLObject.cpp

dolfin/io/XMLObject.h

dolfin/io/XMLParameterList.cpp

dolfin/io/XMLParameterList.h

dolfin/io/XMLVector.cpp

dolfin/io/XMLVector.h

dolfin/io/dolfin_io.h

dolfin/la

dolfin/la/AssemblyMatrix.h

dolfin/la/GMRES.cpp

dolfin/la/GMRES.h

dolfin/la/GenericMatrix.h

dolfin/la/GenericSparsityPattern.h

dolfin/la/GenericTensor.h

dolfin/la/GenericVector.h

dolfin/la/KrylovMethod.h

dolfin/la/KrylovSolver.h

dolfin/la/LU.cpp

dolfin/la/LU.h

dolfin/la/LUSolver.h

dolfin/la/LinearAlgebraFactory.h

dolfin/la/LinearSolver.h

dolfin/la/Matrix.h

dolfin/la/PETScFactory.cpp

dolfin/la/PETScFactory.h

dolfin/la/PETScKrylovMatrix.cpp

dolfin/la/PETScKrylovMatrix.h

dolfin/la/PETScKrylovSolver.cpp

dolfin/la/PETScKrylovSolver.h

dolfin/la/PETScLUSolver.cpp

dolfin/la/PETScLUSolver.h

dolfin/la/PETScLinearSolver.h

dolfin/la/PETScMatrix.cpp

dolfin/la/PETScMatrix.h

dolfin/la/PETScObject.h

dolfin/la/PETScPreconditioner.cpp

dolfin/la/PETScPreconditioner.h

dolfin/la/PETScVector.cpp

dolfin/la/PETScVector.h

dolfin/la/Preconditioner.h

dolfin/la/SLEPcEigenvalueSolver.cpp

dolfin/la/SLEPcEigenvalueSolver.h

dolfin/la/Scalar.h

dolfin/la/SparsityPattern.cpp

dolfin/la/SparsityPattern.h

dolfin/la/Vector.h

dolfin/la/VectorNormType.h

dolfin/la/default_la_types.h

dolfin/la/dolfin_la.h

dolfin/la/solve.cpp

dolfin/la/solve.h

dolfin/la/uBlasDenseMatrix.h

dolfin/la/uBlasDummyPreconditioner.cpp

dolfin/la/uBlasDummyPreconditioner.h

dolfin/la/uBlasFactory.cpp

dolfin/la/uBlasFactory.h

dolfin/la/uBlasILUPreconditioner.cpp

dolfin/la/uBlasILUPreconditioner.h

dolfin/la/uBlasKrylovMatrix.cpp

dolfin/la/uBlasKrylovMatrix.h

dolfin/la/uBlasKrylovSolver.cpp

dolfin/la/uBlasKrylovSolver.h

dolfin/la/uBlasLUSolver.cpp

dolfin/la/uBlasLUSolver.h

dolfin/la/uBlasLinearSolver.h

dolfin/la/uBlasMatrix.cpp

dolfin/la/uBlasMatrix.h

dolfin/la/uBlasPreconditioner.h

dolfin/la/uBlasSparseMatrix.h

dolfin/la/uBlasVector.cpp

dolfin/la/uBlasVector.h

dolfin/la/ublas.h

dolfin/log

dolfin/log/Event.cpp

dolfin/log/Event.h

dolfin/log/LogManager.cpp

dolfin/log/LogManager.h

dolfin/log/LogStream.cpp

dolfin/log/LogStream.h

dolfin/log/Logger.cpp

dolfin/log/Logger.h

dolfin/log/LoggerManager.cpp

dolfin/log/Progress.cpp

dolfin/log/Progress.h

dolfin/log/dolfin_log.h

dolfin/log/log.cpp

dolfin/log/log.h

dolfin/main

dolfin/main/MPI.cpp

dolfin/main/MPI.h

dolfin/main/SubSystemsManager.cpp

dolfin/main/SubSystemsManager.h

dolfin/main/constants.h

dolfin/main/dolfin.h

dolfin/main/dolfin_doc.h

dolfin/main/dolfin_main.h

dolfin/main/init.cpp

dolfin/main/init.h

dolfin/math

dolfin/math/Lagrange.cpp

dolfin/math/Lagrange.h

dolfin/math/Legendre.cpp

dolfin/math/Legendre.h

dolfin/math/basic.cpp

dolfin/math/basic.h

dolfin/math/dolfin_math.h

dolfin/mesh

dolfin/mesh/BoundaryComputation.cpp

dolfin/mesh/BoundaryComputation.h

dolfin/mesh/BoundaryMesh.cpp

dolfin/mesh/BoundaryMesh.h

dolfin/mesh/Cell.cpp

dolfin/mesh/Cell.h

dolfin/mesh/CellType.cpp

dolfin/mesh/CellType.h

dolfin/mesh/Edge.cpp

dolfin/mesh/Edge.h

dolfin/mesh/Face.cpp

dolfin/mesh/Face.h

dolfin/mesh/Facet.cpp

dolfin/mesh/Facet.h

dolfin/mesh/GTSInterface.cpp

dolfin/mesh/GTSInterface.h

dolfin/mesh/GeometricPredicates.cpp

dolfin/mesh/GeometricPredicates.h

dolfin/mesh/IntersectionDetector.cpp

dolfin/mesh/IntersectionDetector.h

dolfin/mesh/IntervalCell.cpp

dolfin/mesh/IntervalCell.h

dolfin/mesh/LocalMeshCoarsening.cpp

dolfin/mesh/LocalMeshCoarsening.h

dolfin/mesh/LocalMeshRefinement.cpp

dolfin/mesh/LocalMeshRefinement.h

dolfin/mesh/MPIMeshCommunicator.cpp

dolfin/mesh/MPIMeshCommunicator.h

dolfin/mesh/Mesh.cpp

dolfin/mesh/Mesh.h

dolfin/mesh/MeshConnectivity.cpp

dolfin/mesh/MeshConnectivity.h

dolfin/mesh/MeshData.cpp

dolfin/mesh/MeshData.h

dolfin/mesh/MeshEditor.cpp

dolfin/mesh/MeshEditor.h

dolfin/mesh/MeshEntity.cpp

dolfin/mesh/MeshEntity.h

dolfin/mesh/MeshEntityIterator.cpp

dolfin/mesh/MeshEntityIterator.h

dolfin/mesh/MeshFunction.h

dolfin/mesh/MeshGeometry.cpp

dolfin/mesh/MeshGeometry.h

dolfin/mesh/MeshHierarchy.cpp

dolfin/mesh/MeshHierarchy.h

dolfin/mesh/MeshHierarchyAlgorithms.cpp

dolfin/mesh/MeshHierarchyAlgorithms.h

dolfin/mesh/MeshOrdering.cpp

dolfin/mesh/MeshOrdering.h

dolfin/mesh/MeshPartition.cpp

dolfin/mesh/MeshPartition.h

dolfin/mesh/MeshTopology.cpp

dolfin/mesh/MeshTopology.h

dolfin/mesh/Point.cpp

dolfin/mesh/Point.h

dolfin/mesh/PointCell.cpp

dolfin/mesh/PointCell.h

dolfin/mesh/SubDomain.cpp

dolfin/mesh/SubDomain.h

dolfin/mesh/TetrahedronCell.cpp

dolfin/mesh/TetrahedronCell.h

dolfin/mesh/TopologyComputation.cpp

dolfin/mesh/TopologyComputation.h

dolfin/mesh/TriangleCell.cpp

dolfin/mesh/TriangleCell.h

dolfin/mesh/UniformMeshRefinement.cpp

dolfin/mesh/UniformMeshRefinement.h

dolfin/mesh/UnitCube.cpp

dolfin/mesh/UnitCube.h

dolfin/mesh/UnitInterval.cpp

dolfin/mesh/UnitInterval.h

dolfin/mesh/UnitSquare.cpp

dolfin/mesh/UnitSquare.h

dolfin/mesh/Vertex.cpp

dolfin/mesh/Vertex.h

dolfin/mesh/dolfin_mesh.h

dolfin/mesh/predicates_init.h

dolfin/mesh/rounding.h

dolfin/mf

dolfin/mf/ConvectionMatrix.h

dolfin/mf/LoadVector.h

dolfin/mf/MassMatrix.h

dolfin/mf/MatrixFactory.cpp

dolfin/mf/MatrixFactory.h

dolfin/mf/StiffnessMatrix.h

dolfin/mf/dolfin_mf.h

dolfin/mf/ffc-forms

dolfin/mf/ffc-forms/ConvectionMatrix2D.form

dolfin/mf/ffc-forms/ConvectionMatrix2D.h

dolfin/mf/ffc-forms/ConvectionMatrix3D.form

dolfin/mf/ffc-forms/ConvectionMatrix3D.h

dolfin/mf/ffc-forms/LoadVector2D.form

dolfin/mf/ffc-forms/LoadVector2D.h

dolfin/mf/ffc-forms/LoadVector3D.form

dolfin/mf/ffc-forms/LoadVector3D.h

dolfin/mf/ffc-forms/MassMatrix2D.form

dolfin/mf/ffc-forms/MassMatrix2D.h

dolfin/mf/ffc-forms/MassMatrix3D.form

dolfin/mf/ffc-forms/MassMatrix3D.h

dolfin/mf/ffc-forms/StiffnessMatrix2D.form

dolfin/mf/ffc-forms/StiffnessMatrix2D.h

dolfin/mf/ffc-forms/StiffnessMatrix3D.form

dolfin/mf/ffc-forms/StiffnessMatrix3D.h

dolfin/nls

dolfin/nls/NewtonSolver.cpp

dolfin/nls/NewtonSolver.h

dolfin/nls/NonlinearProblem.cpp

dolfin/nls/NonlinearProblem.h

dolfin/nls/dolfin_nls.h

dolfin/ode

dolfin/ode/Adaptivity.cpp

dolfin/ode/Adaptivity.h

dolfin/ode/Alloc.cpp

dolfin/ode/Alloc.h

dolfin/ode/ComplexODE.cpp

dolfin/ode/ComplexODE.h

dolfin/ode/Controller.cpp

dolfin/ode/Controller.h

dolfin/ode/Dependencies.cpp

dolfin/ode/Dependencies.h

dolfin/ode/Dual.cpp

dolfin/ode/Dual.h

dolfin/ode/Homotopy.cpp

dolfin/ode/Homotopy.h

dolfin/ode/HomotopyJacobian.cpp

dolfin/ode/HomotopyJacobian.h

dolfin/ode/HomotopyODE.cpp

dolfin/ode/HomotopyODE.h

dolfin/ode/Method.cpp

dolfin/ode/Method.h

dolfin/ode/MonoAdaptiveFixedPointSolver.cpp

dolfin/ode/MonoAdaptiveFixedPointSolver.h

dolfin/ode/MonoAdaptiveJacobian.cpp

dolfin/ode/MonoAdaptiveJacobian.h

dolfin/ode/MonoAdaptiveNewtonSolver.cpp

dolfin/ode/MonoAdaptiveNewtonSolver.h

dolfin/ode/MonoAdaptiveTimeSlab.cpp

dolfin/ode/MonoAdaptiveTimeSlab.h

dolfin/ode/MonoAdaptivity.cpp

dolfin/ode/MonoAdaptivity.h

dolfin/ode/MultiAdaptiveFixedPointSolver.cpp

dolfin/ode/MultiAdaptiveFixedPointSolver.h

dolfin/ode/MultiAdaptiveJacobian.cpp

dolfin/ode/MultiAdaptiveJacobian.h

dolfin/ode/MultiAdaptiveNewtonSolver.cpp

dolfin/ode/MultiAdaptiveNewtonSolver.h

dolfin/ode/MultiAdaptivePreconditioner.cpp

dolfin/ode/MultiAdaptivePreconditioner.h

dolfin/ode/MultiAdaptiveTimeSlab.cpp

dolfin/ode/MultiAdaptiveTimeSlab.h

dolfin/ode/MultiAdaptivity.cpp

dolfin/ode/MultiAdaptivity.h

dolfin/ode/ODE.cpp

dolfin/ode/ODE.h

dolfin/ode/ODESolver.cpp

dolfin/ode/ODESolver.h

dolfin/ode/Partition.cpp

dolfin/ode/Partition.h

dolfin/ode/README

dolfin/ode/ReducedModel.cpp

dolfin/ode/ReducedModel.h

dolfin/ode/Sample.cpp

dolfin/ode/Sample.h

dolfin/ode/TimeSlab.cpp

dolfin/ode/TimeSlab.h

dolfin/ode/TimeSlabJacobian.cpp

dolfin/ode/TimeSlabJacobian.h

dolfin/ode/TimeSlabSolver.cpp

dolfin/ode/TimeSlabSolver.h

dolfin/ode/TimeStepper.cpp

dolfin/ode/TimeStepper.h

dolfin/ode/UpdatedMultiAdaptiveJacobian.cpp

dolfin/ode/UpdatedMultiAdaptiveJacobian.h

dolfin/ode/cGqMethod.cpp

dolfin/ode/cGqMethod.h

dolfin/ode/dGqMethod.cpp

dolfin/ode/dGqMethod.h

dolfin/ode/dolfin_ode.h

dolfin/parameter

dolfin/parameter/DefaultParameters.h

dolfin/parameter/Parameter.cpp

dolfin/parameter/Parameter.h

dolfin/parameter/ParameterList.cpp

dolfin/parameter/ParameterList.h

dolfin/parameter/ParameterSystem.cpp

dolfin/parameter/ParameterSystem.h

dolfin/parameter/ParameterValue.cpp

dolfin/parameter/ParameterValue.h

dolfin/parameter/Parametrized.cpp

dolfin/parameter/Parametrized.h

dolfin/parameter/dolfin_parameter.h

dolfin/parameter/parameters.cpp

dolfin/parameter/parameters.h

dolfin/pde

dolfin/pde/LinearPDE.cpp

dolfin/pde/LinearPDE.h

dolfin/pde/NonlinearPDE.cpp

dolfin/pde/NonlinearPDE.h

dolfin/pde/dolfin_pde.h

dolfin/plot

dolfin/plot/dolfin_plot.h

dolfin/plot/plot.cpp

dolfin/plot/plot.h

dolfin/quadrature

dolfin/quadrature/GaussQuadrature.cpp

dolfin/quadrature/GaussQuadrature.h

dolfin/quadrature/GaussianQuadrature.cpp

dolfin/quadrature/GaussianQuadrature.h

dolfin/quadrature/LobattoQuadrature.cpp

dolfin/quadrature/LobattoQuadrature.h

dolfin/quadrature/Quadrature.cpp

dolfin/quadrature/Quadrature.h

dolfin/quadrature/RadauQuadrature.cpp

dolfin/quadrature/RadauQuadrature.h

dolfin/quadrature/dolfin_quadrature.h

dolfin/scons.cfg

dolfin/swig

dolfin/swig/README

dolfin/swig/directors.i

dolfin/swig/dolfin.i

dolfin/swig/dolfin_common_post.i

dolfin/swig/dolfin_docstrings.i

dolfin/swig/dolfin_exceptions.i

dolfin/swig/dolfin_fem_pre.i

dolfin/swig/dolfin_function_pre.i

dolfin/swig/dolfin_headers.h

dolfin/swig/dolfin_la_post.i

dolfin/swig/dolfin_la_pre.i

dolfin/swig/dolfin_log_post.i

dolfin/swig/dolfin_mesh_post.i

dolfin/swig/dolfin_mesh_pre.i

dolfin/swig/dolfin_pde_pre.i

dolfin/swig/generate.py

dolfin/swig/generate_docstrings.py

dolfin/swig/ignores.i

dolfin/swig/numpy_typemaps.i

dolfin/swig/renames.i

dolfin/swig/typemaps.i

misc

misc/gendoc.sh

misc/greeting

misc/greeting/greeting.sh

misc/petsc.conf

misc/slepc.conf

misc/utils

misc/utils/convert

misc/utils/convert/dolfin-convert

misc/utils/convert/test_diffpack.grid

misc/utils/convert/test_exodus.exo

misc/utils/convert/test_gmsh.msh

misc/utils/convert/test_old_xml.xml

misc/utils/convert/test_tetgen.mesh

misc/utils/emacs

misc/utils/emacs/macros

misc/utils/gid

misc/utils/gid/dolfin.bas

misc/utils/inp2dx

misc/utils/inp2dx/inp2dx.c

misc/utils/inp2dx/inp2dxanim.c

misc/utils/matlab

misc/utils/matlab/meshindex.m

misc/utils/matlab/plotcontroller.m

misc/utils/matlab/plotslab.m

misc/utils/matlab/writegid.m

misc/utils/matlab/writeinp.m

misc/utils/matlab/xmlmatrix.m

misc/utils/matlab/xmlmesh.m

misc/utils/matlab/xmlvector.m

misc/utils/octave

misc/utils/octave/README

misc/utils/octave/pdemesh.m

misc/utils/octave/pdeplot.m

misc/utils/octave/pdesurf.m

misc/utils/opendx

misc/utils/opendx/dolfin.cfg

misc/utils/opendx/dolfin.net

misc/utils/swig

misc/utils/swig/dolfin-swig

misc/utils/system

misc/utils/system/monitor

misc/utils/vim

misc/utils/vim/macros

misc/utils/xml

misc/utils/xml/convertall

misc/utils/xml/inp2xml

sandbox

sandbox/README

sandbox/bdm

sandbox/bdm/MixedPoisson.form

sandbox/bdm/MixedPoisson.h

sandbox/bdm/main.cpp

sandbox/dg

sandbox/dg/Poisson.form

sandbox/dg/Poisson.h

sandbox/dg/Projection.form

sandbox/dg/Projection.h

sandbox/dg/cg-dg-comparison

sandbox/dg/cg-dg-comparison/cg

sandbox/dg/cg-dg-comparison/cg/Poisson.form

sandbox/dg/cg-dg-comparison/cg/Poisson.h

sandbox/dg/cg-dg-comparison/cg/main.cpp

sandbox/dg/cg-dg-comparison/cg/poisson000000.vtu

sandbox/dg/cg-dg-comparison/cg/poissonCG_gamma100_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/cg/poissonCG_gamma100_mesh5000000.vtu

sandbox/dg/cg-dg-comparison/cg/poissonCG_stabilised_gamma4_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/cg/poissonCG_stabilised_gamma4_mesh5000000.vtu

sandbox/dg/cg-dg-comparison/dg

sandbox/dg/cg-dg-comparison/dg/Poisson.form

sandbox/dg/cg-dg-comparison/dg/Poisson.h

sandbox/dg/cg-dg-comparison/dg/Projection.form

sandbox/dg/cg-dg-comparison/dg/Projection.h

sandbox/dg/cg-dg-comparison/dg/main.cpp

sandbox/dg/cg-dg-comparison/dg/poissonDG_gamma12_alpha4_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_gamma24_alpha8_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma12_alpha4_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma12_alpha4_mesh5000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma24_alpha8_mesh5000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha2_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha2_mesh5000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha4_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha4_mesh5000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma8_alpha4_mesh10000000.vtu

sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma8_alpha4_mesh5000000.vtu

sandbox/dg/main.cpp

sandbox/dg/plot.py

sandbox/graph

sandbox/graph/main.cpp

sandbox/jit

sandbox/jit/test.py

sandbox/meshordering

sandbox/meshordering/main.cpp

sandbox/meshordering/meshreordering

sandbox/meshordering/test.form

sandbox/misc

sandbox/misc/main.cpp

sandbox/partitioning

sandbox/partitioning/bench1.sh

sandbox/partitioning/bench2.sh

sandbox/partitioning/bench3.sh

sandbox/partitioning/main.cpp

sandbox/partitioning/partition.h

sandbox/partitioning/plot.py

sandbox/partitioning/plot1a.sh

sandbox/partitioning/plot1b.sh

sandbox/partitioning/plot2a.sh

sandbox/partitioning/plot2b.sh

sandbox/partitioning/plot3a.sh

sandbox/partitioning/plot3b.sh

sandbox/partitioning/unitcube4.xml

sandbox/partitioning/unitsquare40.xml

sandbox/passembly

sandbox/passembly/PdofMap.h

sandbox/passembly/Poisson2D.form

sandbox/passembly/Poisson2D.h

sandbox/passembly/main.cpp

sandbox/passembly/partition.h

scons

scons/simula-scons

scons/simula-scons/AUTHORS

scons/simula-scons/README

scons/simula-scons/TODO

scons/simula-scons/setup.py

scons/simula-scons/simula_scons

scons/simula-scons/simula_scons/Customize.py

scons/simula-scons/simula_scons/Errors.py

scons/simula-scons/simula_scons/__init__.py

scons/simula-scons/simula_scons/_module.py

scons/simula-scons/simula_scons/latex.py

scons/simula-scons/simula_scons/pkgconfig.py

scons/simula-scons/simula_scons/pkgconfiggenerators

scons/simula-scons/simula_scons/pkgconfiggenerators/__init__.py

scons/simula-scons/simula_scons/pkgconfiggenerators/boost.py

scons/simula-scons/simula_scons/pkgconfiggenerators/commonPkgConfigUtils.py

scons/simula-scons/simula_scons/pkgconfiggenerators/dolfin.py

scons/simula-scons/simula_scons/pkgconfiggenerators/hypre.py

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/boost

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/boost/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/cmake

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/cmake/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/dolfin

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/dolfin/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/hypre

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/hypre/hypre-configure

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/hypre/hypre-struct_overlap_innerprod.c

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/hypre/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/pkgconfig

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/pkgconfig/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/scotch

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/scotch/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/trilinos

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/trilinos/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/ufc

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/ufc/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/vtk

scons/simula-scons/simula_scons/pkgconfiggenerators/install_packages/vtk/install.sh

scons/simula-scons/simula_scons/pkgconfiggenerators/numeric.py

scons/simula-scons/simula_scons/pkgconfiggenerators/numpy.py

scons/simula-scons/simula_scons/pkgconfiggenerators/petsc.py

scons/simula-scons/simula_scons/pkgconfiggenerators/python.py

scons/simula-scons/simula_scons/pkgconfiggenerators/scotch.py

scons/simula-scons/simula_scons/pkgconfiggenerators/slepc.py

scons/simula-scons/simula_scons/pkgconfiggenerators/superlu.py

scons/simula-scons/simula_scons/pkgconfiggenerators/trilinos.py

scons/simula-scons/simula_scons/pkgconfiggenerators/umfpack.py

site-packages

site-packages/dolfin

site-packages/dolfin/__init__.py

site-packages/dolfin/assemble.py

site-packages/dolfin/constants.py

site-packages/dolfin/plot.py

test

test/function

test/function/cpp

test/function/cpp/test.cpp

test/function/python

test/function/python/test.py

test/graph

test/graph/cpp

test/graph/cpp/test.cpp

test/graph/python

test/graph/python/test.py

test/mesh

test/mesh/cpp

test/mesh/cpp/test.cpp

test/mesh/python

test/mesh/python/test.py

test/test.py

files removed:
Makefile.am

Makefile.in

NEWS

aclocal.m4

config.guess

config.sub

configure

configure.ac

configure.local

depcomp

doc/manual/Makefile

dolfin.pc.in

gendoc.sh

install-sh

ltmain.sh

m4

m4/ac_pkg_swig.m4

m4/ac_python_devel.m4

m4/ax_boost_base.m4

m4/ax_compiler_vendor.m4

m4/libtool.m4

m4/libxml.m4

missing

mkinstalldirs

numpy.conf

petsc.conf

py-compile

slepc.conf

src

src/Makefile.am

src/Makefile.in

src/bench

src/bench/Makefile.am

src/bench/Makefile.in

src/bench/README

src/bench/bench

src/bench/fem

src/bench/fem/Makefile.am

src/bench/fem/Makefile.in

src/bench/fem/assembly

src/bench/fem/assembly/Advection.form

src/bench/fem/assembly/Advection.h

src/bench/fem/assembly/Makefile

src/bench/fem/assembly/bench.log

src/bench/fem/assembly/bench.py

src/bench/fem/assembly/main.cpp

src/bench/fem/convergence

src/bench/fem/convergence/Makefile

src/bench/fem/convergence/Poisson2D_1.form

src/bench/fem/convergence/Poisson2D_1.h

src/bench/fem/convergence/Poisson2D_2.form

src/bench/fem/convergence/Poisson2D_2.h

src/bench/fem/convergence/Poisson2D_3.form

src/bench/fem/convergence/Poisson2D_3.h

src/bench/fem/convergence/Poisson2D_4.form

src/bench/fem/convergence/Poisson2D_4.h

src/bench/fem/convergence/Poisson2D_5.form

src/bench/fem/convergence/Poisson2D_5.h

src/bench/fem/convergence/Poisson3D_1.form

src/bench/fem/convergence/Poisson3D_1.h

src/bench/fem/convergence/Poisson3D_2.form

src/bench/fem/convergence/Poisson3D_2.h

src/bench/fem/convergence/Poisson3D_3.form

src/bench/fem/convergence/Poisson3D_3.h

src/bench/fem/convergence/Poisson3D_4.form

src/bench/fem/convergence/Poisson3D_4.h

src/bench/fem/convergence/Poisson3D_5.form

src/bench/fem/convergence/Poisson3D_5.h

src/bench/fem/convergence/README

src/bench/fem/convergence/bench.log

src/bench/fem/convergence/bench.py

src/bench/fem/convergence/main.cpp

src/bench/fem/passembly

src/bench/fem/passembly/Makefile

src/bench/fem/passembly/Nonlinear2D.form

src/bench/fem/passembly/Nonlinear2D.h

src/bench/fem/passembly/Poisson.form

src/bench/fem/passembly/Poisson.h

src/bench/fem/passembly/Poisson2D.h

src/bench/fem/passembly/Poisson3D_1.form

src/bench/fem/passembly/Poisson3D_1.h

src/bench/fem/passembly/assemble.h

src/bench/fem/passembly/getopts.cpp

src/bench/fem/passembly/getopts.h

src/bench/fem/passembly/main.cpp

src/bench/fem/passembly/parallel_poisson_cube.sh

src/bench/fem/passembly/plot.py

src/bench/fem/passembly/plot_parallel_assembly_time.sh

src/bench/fem/passembly/sequential_poisson_cube.sh

src/bench/la

src/bench/la/Makefile.am

src/bench/la/Makefile.in

src/bench/la/bench.log

src/bench/la/bench.py

src/bench/la/sparse-matrix

src/bench/la/sparse-matrix/Makefile

src/bench/la/sparse-matrix/Poisson.form.old

src/bench/la/sparse-matrix/Poisson.h

src/bench/la/sparse-matrix/VectorPoisson.form.old

src/bench/la/sparse-matrix/VectorPoisson.h

src/bench/la/sparse-matrix/main.cpp

src/bench/la/vector

src/bench/la/vector/Makefile

src/bench/la/vector/main.cpp

src/bench/mesh

src/bench/mesh/Makefile

src/bench/mesh/bench.log

src/bench/mesh/bench.py

src/bench/mesh/main.cpp

src/bench/ode

src/bench/ode/Makefile.am

src/bench/ode/Makefile.in

src/bench/ode/reaction

src/bench/ode/reaction/Makefile

src/bench/ode/reaction/README

src/bench/ode/reaction/bench-domain.log

src/bench/ode/reaction/bench-domain.py

src/bench/ode/reaction/bench-overhead.log

src/bench/ode/reaction/bench-overhead.py

src/bench/ode/reaction/bench-plot.py

src/bench/ode/reaction/bench-tol.log

src/bench/ode/reaction/bench-tol.py

src/bench/ode/reaction/bench.log

src/bench/ode/reaction/bench.py

src/bench/ode/reaction/benchutil.py

src/bench/ode/reaction/checkerror.py

src/bench/ode/reaction/main.cpp

src/bench/ode/reaction/parameters-bench.xml

src/bench/ode/reaction/parameters-plot.xml

src/bench/ode/reaction/parameters-reference.xml

src/bench/ode/reaction/reference_1000.data

src/bench/ode/reaction/reference_16000.data

src/bench/ode/reaction/reference_2000.data

src/bench/ode/reaction/reference_4000.data

src/bench/ode/reaction/reference_8000.data

src/bench/ode/wave

src/bench/ode/wave/Makefile

src/bench/ode/wave/bench.log

src/bench/ode/wave/bench.py

src/bench/ode/wave/main.cpp

src/bench/ode/wave/parameters-bench.xml

src/bench/ode/wave/slit.xml.gz

src/demo

src/demo/Makefile.am

src/demo/Makefile.in

src/demo/fem

src/demo/fem/assembly

src/demo/fem/assembly/cpp

src/demo/fem/assembly/cpp/Makefile

src/demo/fem/assembly/cpp/ReactionDiffusion.form

src/demo/fem/assembly/cpp/ReactionDiffusion.h

src/demo/fem/assembly/cpp/main.cpp

src/demo/fem/assembly/python

src/demo/fem/assembly/python/README

src/demo/fem/simple

src/demo/fem/simple/cpp

src/demo/fem/simple/cpp/Makefile

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src/kernel/math/Legendre.cpp

src/kernel/math/Makefile.am

src/kernel/math/Makefile.in

src/kernel/math/basic.cpp

src/kernel/math/dolfin

src/kernel/math/dolfin/Lagrange.h

src/kernel/math/dolfin/Legendre.h

src/kernel/math/dolfin/Makefile.am

src/kernel/math/dolfin/Makefile.in

src/kernel/math/dolfin/basic.h

src/kernel/math/dolfin/dolfin_math.h

src/kernel/mesh

src/kernel/mesh/BoundaryComputation.cpp

src/kernel/mesh/BoundaryMesh.cpp

src/kernel/mesh/Cell.cpp

src/kernel/mesh/CellType.cpp

src/kernel/mesh/Edge.cpp

src/kernel/mesh/Face.cpp

src/kernel/mesh/Facet.cpp

src/kernel/mesh/GTSInterface.cpp

src/kernel/mesh/GeometricPredicates.cpp

src/kernel/mesh/IntersectionDetector.cpp

src/kernel/mesh/IntervalCell.cpp

src/kernel/mesh/LocalMeshCoarsening.cpp

src/kernel/mesh/LocalMeshRefinement.cpp

src/kernel/mesh/MPIMeshCommunicator.cpp

src/kernel/mesh/Makefile.am

src/kernel/mesh/Makefile.in

src/kernel/mesh/Mesh.cpp

src/kernel/mesh/MeshConnectivity.cpp

src/kernel/mesh/MeshData.cpp

src/kernel/mesh/MeshEditor.cpp

src/kernel/mesh/MeshEntity.cpp

src/kernel/mesh/MeshEntityIterator.cpp

src/kernel/mesh/MeshGeometry.cpp

src/kernel/mesh/MeshHierarchy.cpp

src/kernel/mesh/MeshHierarchyAlgorithms.cpp

src/kernel/mesh/MeshOrdering.cpp

src/kernel/mesh/MeshPartition.cpp

src/kernel/mesh/MeshTopology.cpp

src/kernel/mesh/Point.cpp

src/kernel/mesh/PointCell.cpp

src/kernel/mesh/SubDomain.cpp

src/kernel/mesh/TetrahedronCell.cpp

src/kernel/mesh/TopologyComputation.cpp

src/kernel/mesh/TriangleCell.cpp

src/kernel/mesh/UniformMeshRefinement.cpp

src/kernel/mesh/UnitCube.cpp

src/kernel/mesh/UnitInterval.cpp

src/kernel/mesh/UnitSquare.cpp

src/kernel/mesh/Vertex.cpp

src/kernel/mesh/dolfin

src/kernel/mesh/dolfin/BoundaryComputation.h

src/kernel/mesh/dolfin/BoundaryMesh.h

src/kernel/mesh/dolfin/Cell.h

src/kernel/mesh/dolfin/CellType.h

src/kernel/mesh/dolfin/Edge.h

src/kernel/mesh/dolfin/Face.h

src/kernel/mesh/dolfin/Facet.h

src/kernel/mesh/dolfin/GTSInterface.h

src/kernel/mesh/dolfin/GeometricPredicates.h

src/kernel/mesh/dolfin/IntersectionDetector.h

src/kernel/mesh/dolfin/IntervalCell.h

src/kernel/mesh/dolfin/LocalMeshCoarsening.h

src/kernel/mesh/dolfin/LocalMeshRefinement.h

src/kernel/mesh/dolfin/MPIMeshCommunicator.h

src/kernel/mesh/dolfin/Makefile.am

src/kernel/mesh/dolfin/Makefile.in

src/kernel/mesh/dolfin/Mesh.h

src/kernel/mesh/dolfin/MeshConnectivity.h

src/kernel/mesh/dolfin/MeshData.h

src/kernel/mesh/dolfin/MeshEditor.h

src/kernel/mesh/dolfin/MeshEntity.h

src/kernel/mesh/dolfin/MeshEntityIterator.h

src/kernel/mesh/dolfin/MeshFunction.h

src/kernel/mesh/dolfin/MeshGeometry.h

src/kernel/mesh/dolfin/MeshHierarchy.h

src/kernel/mesh/dolfin/MeshHierarchyAlgorithms.h

src/kernel/mesh/dolfin/MeshOrdering.h

src/kernel/mesh/dolfin/MeshPartition.h

src/kernel/mesh/dolfin/MeshTopology.h

src/kernel/mesh/dolfin/Point.h

src/kernel/mesh/dolfin/PointCell.h

src/kernel/mesh/dolfin/SubDomain.h

src/kernel/mesh/dolfin/TetrahedronCell.h

src/kernel/mesh/dolfin/TopologyComputation.h

src/kernel/mesh/dolfin/TriangleCell.h

src/kernel/mesh/dolfin/UniformMeshRefinement.h

src/kernel/mesh/dolfin/UnitCube.h

src/kernel/mesh/dolfin/UnitInterval.h

src/kernel/mesh/dolfin/UnitSquare.h

src/kernel/mesh/dolfin/Vertex.h

src/kernel/mesh/dolfin/dolfin_mesh.h

src/kernel/mesh/predicates_init.h

src/kernel/mesh/rounding.h

src/kernel/mf

src/kernel/mf/Makefile.am

src/kernel/mf/Makefile.in

src/kernel/mf/MatrixFactory.cpp

src/kernel/mf/dolfin

src/kernel/mf/dolfin/ConvectionMatrix.h

src/kernel/mf/dolfin/LoadVector.h

src/kernel/mf/dolfin/Makefile.am

src/kernel/mf/dolfin/Makefile.in

src/kernel/mf/dolfin/MassMatrix.h

src/kernel/mf/dolfin/MatrixFactory.h

src/kernel/mf/dolfin/StiffnessMatrix.h

src/kernel/mf/dolfin/dolfin_mf.h

src/kernel/mf/ffc-forms

src/kernel/mf/ffc-forms/ConvectionMatrix2D.form

src/kernel/mf/ffc-forms/ConvectionMatrix2D.h

src/kernel/mf/ffc-forms/ConvectionMatrix3D.form

src/kernel/mf/ffc-forms/ConvectionMatrix3D.h

src/kernel/mf/ffc-forms/LoadVector2D.form

src/kernel/mf/ffc-forms/LoadVector2D.h

src/kernel/mf/ffc-forms/LoadVector3D.form

src/kernel/mf/ffc-forms/LoadVector3D.h

src/kernel/mf/ffc-forms/MassMatrix2D.form

src/kernel/mf/ffc-forms/MassMatrix2D.h

src/kernel/mf/ffc-forms/MassMatrix3D.form

src/kernel/mf/ffc-forms/MassMatrix3D.h

src/kernel/mf/ffc-forms/StiffnessMatrix2D.form

src/kernel/mf/ffc-forms/StiffnessMatrix2D.h

src/kernel/mf/ffc-forms/StiffnessMatrix3D.form

src/kernel/mf/ffc-forms/StiffnessMatrix3D.h

src/kernel/nls

src/kernel/nls/Makefile.am

src/kernel/nls/Makefile.in

src/kernel/nls/NewtonSolver.cpp

src/kernel/nls/NonlinearProblem.cpp

src/kernel/nls/dolfin

src/kernel/nls/dolfin/Makefile.am

src/kernel/nls/dolfin/Makefile.in

src/kernel/nls/dolfin/NewtonSolver.h

src/kernel/nls/dolfin/NonlinearProblem.h

src/kernel/nls/dolfin/dolfin_nls.h

src/kernel/ode

src/kernel/ode/Adaptivity.cpp

src/kernel/ode/Alloc.cpp

src/kernel/ode/ComplexODE.cpp

src/kernel/ode/Controller.cpp

src/kernel/ode/Dependencies.cpp

src/kernel/ode/Dual.cpp

src/kernel/ode/Homotopy.cpp

src/kernel/ode/HomotopyJacobian.cpp

src/kernel/ode/HomotopyODE.cpp

src/kernel/ode/Makefile.am

src/kernel/ode/Makefile.in

src/kernel/ode/Method.cpp

src/kernel/ode/MonoAdaptiveFixedPointSolver.cpp

src/kernel/ode/MonoAdaptiveJacobian.cpp

src/kernel/ode/MonoAdaptiveNewtonSolver.cpp

src/kernel/ode/MonoAdaptiveTimeSlab.cpp

src/kernel/ode/MonoAdaptivity.cpp

src/kernel/ode/MultiAdaptiveFixedPointSolver.cpp

src/kernel/ode/MultiAdaptiveJacobian.cpp

src/kernel/ode/MultiAdaptiveNewtonSolver.cpp

src/kernel/ode/MultiAdaptivePreconditioner.cpp

src/kernel/ode/MultiAdaptiveTimeSlab.cpp

src/kernel/ode/MultiAdaptivity.cpp

src/kernel/ode/ODE.cpp

src/kernel/ode/ODESolver.cpp

src/kernel/ode/Partition.cpp

src/kernel/ode/README

src/kernel/ode/ReducedModel.cpp

src/kernel/ode/Sample.cpp

src/kernel/ode/TimeSlab.cpp

src/kernel/ode/TimeSlabJacobian.cpp

src/kernel/ode/TimeSlabSolver.cpp

src/kernel/ode/TimeStepper.cpp

src/kernel/ode/UpdatedMultiAdaptiveJacobian.cpp

src/kernel/ode/cGqMethod.cpp

src/kernel/ode/dGqMethod.cpp

src/kernel/ode/dolfin

src/kernel/ode/dolfin/Adaptivity.h

src/kernel/ode/dolfin/Alloc.h

src/kernel/ode/dolfin/ComplexODE.h

src/kernel/ode/dolfin/Controller.h

src/kernel/ode/dolfin/Dependencies.h

src/kernel/ode/dolfin/Dual.h

src/kernel/ode/dolfin/Homotopy.h

src/kernel/ode/dolfin/HomotopyJacobian.h

src/kernel/ode/dolfin/HomotopyODE.h

src/kernel/ode/dolfin/Makefile.am

src/kernel/ode/dolfin/Makefile.in

src/kernel/ode/dolfin/Method.h

src/kernel/ode/dolfin/MonoAdaptiveFixedPointSolver.h

src/kernel/ode/dolfin/MonoAdaptiveJacobian.h

src/kernel/ode/dolfin/MonoAdaptiveNewtonSolver.h

src/kernel/ode/dolfin/MonoAdaptiveTimeSlab.h

src/kernel/ode/dolfin/MonoAdaptivity.h

src/kernel/ode/dolfin/MultiAdaptiveFixedPointSolver.h

src/kernel/ode/dolfin/MultiAdaptiveJacobian.h

src/kernel/ode/dolfin/MultiAdaptiveNewtonSolver.h

src/kernel/ode/dolfin/MultiAdaptivePreconditioner.h

src/kernel/ode/dolfin/MultiAdaptiveTimeSlab.h

src/kernel/ode/dolfin/MultiAdaptivity.h

src/kernel/ode/dolfin/ODE.h

src/kernel/ode/dolfin/ODESolver.h

src/kernel/ode/dolfin/Partition.h

src/kernel/ode/dolfin/ReducedModel.h

src/kernel/ode/dolfin/Sample.h

src/kernel/ode/dolfin/TimeSlab.h

src/kernel/ode/dolfin/TimeSlabJacobian.h

src/kernel/ode/dolfin/TimeSlabSolver.h

src/kernel/ode/dolfin/TimeStepper.h

src/kernel/ode/dolfin/UpdatedMultiAdaptiveJacobian.h

src/kernel/ode/dolfin/cGqMethod.h

src/kernel/ode/dolfin/dGqMethod.h

src/kernel/ode/dolfin/dolfin_ode.h

src/kernel/parameter

src/kernel/parameter/Makefile.am

src/kernel/parameter/Makefile.in

src/kernel/parameter/Parameter.cpp

src/kernel/parameter/ParameterList.cpp

src/kernel/parameter/ParameterSystem.cpp

src/kernel/parameter/ParameterValue.cpp

src/kernel/parameter/Parametrized.cpp

src/kernel/parameter/dolfin

src/kernel/parameter/dolfin/DefaultParameters.h

src/kernel/parameter/dolfin/Makefile.am

src/kernel/parameter/dolfin/Makefile.in

src/kernel/parameter/dolfin/Parameter.h

src/kernel/parameter/dolfin/ParameterList.h

src/kernel/parameter/dolfin/ParameterSystem.h

src/kernel/parameter/dolfin/ParameterValue.h

src/kernel/parameter/dolfin/Parametrized.h

src/kernel/parameter/dolfin/dolfin_parameter.h

src/kernel/parameter/dolfin/parameters.h

src/kernel/parameter/parameters.cpp

src/kernel/pde

src/kernel/pde/LinearPDE.cpp

src/kernel/pde/Makefile.am

src/kernel/pde/Makefile.in

src/kernel/pde/NonlinearPDE.cpp

src/kernel/pde/dolfin

src/kernel/pde/dolfin/LinearPDE.h

src/kernel/pde/dolfin/Makefile.am

src/kernel/pde/dolfin/Makefile.in

src/kernel/pde/dolfin/NonlinearPDE.h

src/kernel/pde/dolfin/dolfin_pde.h

src/kernel/plot

src/kernel/plot/Makefile.am

src/kernel/plot/Makefile.in

src/kernel/plot/dolfin

src/kernel/plot/dolfin/Makefile.am

src/kernel/plot/dolfin/Makefile.in

src/kernel/plot/dolfin/dolfin_plot.h

src/kernel/plot/dolfin/plot.h

src/kernel/plot/plot.cpp

src/kernel/quadrature

src/kernel/quadrature/GaussQuadrature.cpp

src/kernel/quadrature/GaussianQuadrature.cpp

src/kernel/quadrature/LobattoQuadrature.cpp

src/kernel/quadrature/Makefile.am

src/kernel/quadrature/Makefile.in

src/kernel/quadrature/Quadrature.cpp

src/kernel/quadrature/RadauQuadrature.cpp

src/kernel/quadrature/dolfin

src/kernel/quadrature/dolfin/GaussQuadrature.h

src/kernel/quadrature/dolfin/GaussianQuadrature.h

src/kernel/quadrature/dolfin/LobattoQuadrature.h

src/kernel/quadrature/dolfin/Makefile.am

src/kernel/quadrature/dolfin/Makefile.in

src/kernel/quadrature/dolfin/Quadrature.h

src/kernel/quadrature/dolfin/RadauQuadrature.h

src/kernel/quadrature/dolfin/dolfin_quadrature.h

src/lib

src/lib/Makefile.am

src/lib/Makefile.in

src/pydolfin

src/pydolfin/Makefile.am

src/pydolfin/Makefile.in

src/pydolfin/README

src/pydolfin/__init__.py

src/pydolfin/assemble.py

src/pydolfin/constants.py

src/pydolfin/directors.i

src/pydolfin/dolfin.i

src/pydolfin/dolfin_common_post.i

src/pydolfin/dolfin_docstrings.i

src/pydolfin/dolfin_exceptions.i

src/pydolfin/dolfin_fem_pre.i

src/pydolfin/dolfin_function_pre.i

src/pydolfin/dolfin_headers.h

src/pydolfin/dolfin_la_post.i

src/pydolfin/dolfin_la_pre.i

src/pydolfin/dolfin_log_post.i

src/pydolfin/dolfin_mesh_post.i

src/pydolfin/dolfin_mesh_pre.i

src/pydolfin/dolfin_pde_pre.i

src/pydolfin/generate.py

src/pydolfin/generate_docstrings.py

src/pydolfin/ignores.i

src/pydolfin/numpy_typemaps.i

src/pydolfin/plot.py

src/pydolfin/renames.i

src/pydolfin/typemaps.i

src/sandbox

src/sandbox/README

src/sandbox/bdm

src/sandbox/bdm/Makefile

src/sandbox/bdm/MixedPoisson.form

src/sandbox/bdm/MixedPoisson.h

src/sandbox/bdm/main.cpp

src/sandbox/dg

src/sandbox/dg/Makefile

src/sandbox/dg/Poisson.form

src/sandbox/dg/Poisson.h

src/sandbox/dg/Projection.form

src/sandbox/dg/Projection.h

src/sandbox/dg/cg-dg-comparison

src/sandbox/dg/cg-dg-comparison/cg

src/sandbox/dg/cg-dg-comparison/cg/Makefile

src/sandbox/dg/cg-dg-comparison/cg/Poisson.form

src/sandbox/dg/cg-dg-comparison/cg/Poisson.h

src/sandbox/dg/cg-dg-comparison/cg/main.cpp

src/sandbox/dg/cg-dg-comparison/cg/poisson000000.vtu

src/sandbox/dg/cg-dg-comparison/cg/poissonCG_gamma100_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/cg/poissonCG_gamma100_mesh5000000.vtu

src/sandbox/dg/cg-dg-comparison/cg/poissonCG_stabilised_gamma4_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/cg/poissonCG_stabilised_gamma4_mesh5000000.vtu

src/sandbox/dg/cg-dg-comparison/dg

src/sandbox/dg/cg-dg-comparison/dg/Makefile

src/sandbox/dg/cg-dg-comparison/dg/Poisson.form

src/sandbox/dg/cg-dg-comparison/dg/Poisson.h

src/sandbox/dg/cg-dg-comparison/dg/Projection.form

src/sandbox/dg/cg-dg-comparison/dg/Projection.h

src/sandbox/dg/cg-dg-comparison/dg/main.cpp

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_gamma12_alpha4_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_gamma24_alpha8_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma12_alpha4_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma12_alpha4_mesh5000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma24_alpha8_mesh5000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha2_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha2_mesh5000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha4_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma4_alpha4_mesh5000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma8_alpha4_mesh10000000.vtu

src/sandbox/dg/cg-dg-comparison/dg/poissonDG_stabilised_gamma8_alpha4_mesh5000000.vtu

src/sandbox/dg/main.cpp

src/sandbox/dg/plot.py

src/sandbox/graph

src/sandbox/graph/Makefile

src/sandbox/graph/main.cpp

src/sandbox/jit

src/sandbox/jit/test.py

src/sandbox/meshordering

src/sandbox/meshordering/Makefile

src/sandbox/meshordering/main.cpp

src/sandbox/meshordering/meshreordering

src/sandbox/meshordering/test.form

src/sandbox/misc

src/sandbox/misc/Makefile

src/sandbox/misc/main.cpp

src/sandbox/partitioning

src/sandbox/partitioning/Makefile

src/sandbox/partitioning/bench1.sh

src/sandbox/partitioning/bench2.sh

src/sandbox/partitioning/bench3.sh

src/sandbox/partitioning/main.cpp

src/sandbox/partitioning/partition.h

src/sandbox/partitioning/plot.py

src/sandbox/partitioning/plot1a.sh

src/sandbox/partitioning/plot1b.sh

src/sandbox/partitioning/plot2a.sh

src/sandbox/partitioning/plot2b.sh

src/sandbox/partitioning/plot3a.sh

src/sandbox/partitioning/plot3b.sh

src/sandbox/partitioning/unitcube4.xml

src/sandbox/partitioning/unitsquare40.xml

src/sandbox/passembly

src/sandbox/passembly/Makefile

src/sandbox/passembly/PdofMap.h

src/sandbox/passembly/Poisson2D.form

src/sandbox/passembly/Poisson2D.h

src/sandbox/passembly/main.cpp

src/sandbox/passembly/partition.h

src/test

src/test/Makefile.am

src/test/Makefile.in

src/test/function

src/test/function/cpp

src/test/function/cpp/Makefile

src/test/function/cpp/test.cpp

src/test/function/python

src/test/function/python/test.py

src/test/graph

src/test/graph/cpp

src/test/graph/cpp/Makefile

src/test/graph/cpp/test.cpp

src/test/graph/python

src/test/graph/python/test.py

src/test/mesh

src/test/mesh/cpp

src/test/mesh/cpp/Makefile

src/test/mesh/cpp/test.cpp

src/test/mesh/python

src/test/mesh/python/test.py

src/test/test.py

src/utils

src/utils/Makefile.am

src/utils/Makefile.in

src/utils/convert

src/utils/convert/Makefile.am

src/utils/convert/Makefile.in

src/utils/convert/dolfin-convert

src/utils/convert/test_diffpack.grid

src/utils/convert/test_exodus.exo

src/utils/convert/test_gmsh.msh

src/utils/convert/test_old_xml.xml

src/utils/convert/test_tetgen.mesh

src/utils/emacs

src/utils/emacs/macros

src/utils/gid

src/utils/gid/dolfin.bas

src/utils/inp2dx

src/utils/inp2dx/Makefile.am

src/utils/inp2dx/Makefile.in

src/utils/inp2dx/inp2dx.c

src/utils/inp2dx/inp2dxanim.c

src/utils/matlab

src/utils/matlab/meshindex.m

src/utils/matlab/plotcontroller.m

src/utils/matlab/plotslab.m

src/utils/matlab/writegid.m

src/utils/matlab/writeinp.m

src/utils/matlab/xmlmatrix.m

src/utils/matlab/xmlmesh.m

src/utils/matlab/xmlvector.m

src/utils/octave

src/utils/octave/README

src/utils/octave/pdemesh.m

src/utils/octave/pdeplot.m

src/utils/octave/pdesurf.m

src/utils/opendx

src/utils/opendx/dolfin.cfg

src/utils/opendx/dolfin.net

src/utils/swig

src/utils/swig/Makefile.am

src/utils/swig/Makefile.in

src/utils/swig/dolfin-swig

src/utils/system

src/utils/system/monitor

src/utils/vim

src/utils/vim/macros

src/utils/xml

src/utils/xml/convertall

src/utils/xml/inp2xml

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added added

removed removed

src/demo/ode/courtemanche/plot.py

1

# Import matplotlib

2

from pylab import *

3

4

# Import solution

5

from solution import *

6

7

# Plot first component of solution

8

subplot(211)

9

plot(t, u[:,0])

10

grid(True)

11

xlabel('t')

12

ylabel('V(t)')

13

title('Courtemanche')

14

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# Plot time steps

16

subplot(212)

17

semilogy(t, k[:,0])

18

grid(True)

19

xlabel('t')

20

ylabel('k(t)')

21

22

# Display value at end time

23

print "V(T) = " + str(u[len(u) - 1, 0])

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show()

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