├── .circleci └── config.yml ├── .github └── workflows │ ├── docs.yml │ └── pypi.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── ChangeLog.rst ├── LICENSE ├── README.md ├── docker └── firedrake │ └── README ├── docs ├── Makefile ├── bin │ └── pylit.py ├── requirements.txt └── source │ ├── _static │ ├── adjoint.html │ ├── burgers_timesteps.png │ ├── burgers_timesteps_expanded.png │ ├── dolfin_adjoint.pdf │ ├── forward.html │ ├── gst.pdf │ ├── libadjoint.pdf │ ├── logo.pdf │ ├── more.png │ ├── optimal_control.py │ ├── optimisation.pdf │ ├── overloading │ │ ├── normalise.py │ │ ├── normalise_overloaded.py │ │ ├── tutorial9.py │ │ └── tutorial9_overloading.py │ ├── poster_funke_2015.pdf │ ├── poster_small_funke_2015.pdf │ ├── pygments.css │ ├── simplified_burgers │ ├── simplified_burgers.png │ ├── simplified_burgers_named │ ├── simplified_burgers_named.png │ ├── slider │ │ ├── klein.png │ │ └── poisson-topology.png │ ├── time-dependent-wave.py │ ├── tutorial1.py │ ├── tutorial2.py │ ├── tutorial3.py │ ├── tutorial4.py │ ├── tutorial7.py │ ├── tutorial7_name_scope.py │ ├── tutorial7_named.py │ └── tutorial8.py │ ├── _themes │ └── dolfin-adjoint │ │ ├── README │ │ ├── layout.html │ │ ├── static │ │ ├── banner.png │ │ ├── banner.svg │ │ ├── dialog-note.png │ │ ├── dialog-seealso.png │ │ ├── dialog-topic.png │ │ ├── dialog-warning.png │ │ ├── epub.css │ │ ├── feature-item-1.png │ │ ├── featured.css │ │ ├── feed-icon-14x14.gif │ │ ├── fenics-book-icon.png │ │ ├── fenics-web.png │ │ ├── fenics.css_t │ │ ├── flexslider │ │ │ ├── README.mdown │ │ │ ├── changelog.txt │ │ │ ├── flexslider.css │ │ │ ├── fonts │ │ │ │ ├── flexslider-icon.eot │ │ │ │ ├── flexslider-icon.svg │ │ │ │ ├── flexslider-icon.ttf │ │ │ │ └── flexslider-icon.woff │ │ │ ├── images │ │ │ │ └── bg_play_pause.png │ │ │ ├── jquery.flexslider-min.js │ │ │ └── jquery.flexslider.js │ │ ├── footerbg.png │ │ ├── headerbg.png │ │ ├── highlight │ │ │ ├── CHANGES.md │ │ │ ├── LICENSE │ │ │ ├── README.md │ │ │ ├── README.ru.md │ │ │ ├── highlight.pack.js │ │ │ └── styles │ │ │ │ ├── arta.css │ │ │ │ ├── ascetic.css │ │ │ │ ├── atelier-dune.dark.css │ │ │ │ ├── atelier-dune.light.css │ │ │ │ ├── atelier-forest.dark.css │ │ │ │ ├── atelier-forest.light.css │ │ │ │ ├── atelier-heath.dark.css │ │ │ │ ├── atelier-heath.light.css │ │ │ │ ├── atelier-lakeside.dark.css │ │ │ │ ├── atelier-lakeside.light.css │ │ │ │ ├── atelier-seaside.dark.css │ │ │ │ ├── atelier-seaside.light.css │ │ │ │ ├── brown_paper.css │ │ │ │ ├── brown_papersq.png │ │ │ │ ├── dark.css │ │ │ │ ├── default.css │ │ │ │ ├── docco.css │ │ │ │ ├── far.css │ │ │ │ ├── foundation.css │ │ │ │ ├── github.css │ │ │ │ ├── googlecode.css │ │ │ │ ├── idea.css │ │ │ │ ├── ir_black.css │ │ │ │ ├── magula.css │ │ │ │ ├── mono-blue.css │ │ │ │ ├── monokai.css │ │ │ │ ├── monokai_sublime.css │ │ │ │ ├── obsidian.css │ │ │ │ ├── paraiso.dark.css │ │ │ │ ├── paraiso.light.css │ │ │ │ ├── pojoaque.css │ │ │ │ ├── pojoaque.jpg │ │ │ │ ├── railscasts.css │ │ │ │ ├── rainbow.css │ │ │ │ ├── school_book.css │ │ │ │ ├── school_book.png │ │ │ │ ├── solarized_dark.css │ │ │ │ ├── solarized_light.css │ │ │ │ ├── sunburst.css │ │ │ │ ├── tomorrow-night-blue.css │ │ │ │ ├── tomorrow-night-bright.css │ │ │ │ ├── tomorrow-night-eighties.css │ │ │ │ ├── tomorrow-night.css │ │ │ │ ├── tomorrow.css │ │ │ │ ├── vs.css │ │ │ │ ├── xcode.css │ │ │ │ └── zenburn.css │ │ ├── icon.ico │ │ ├── icon.png │ │ ├── ie6.css │ │ ├── middlebg.png │ │ ├── neuton-fontfacekit │ │ │ ├── Apache License Version 2.txt │ │ │ ├── Neuton-webfont.eot │ │ │ ├── Neuton-webfont.svg │ │ │ ├── Neuton-webfont.ttf │ │ │ ├── Neuton-webfont.woff │ │ │ ├── demo.html │ │ │ └── stylesheet.css │ │ ├── nobile-fontfacekit │ │ │ ├── SIL Open Font License 1.1.txt │ │ │ ├── demo.html │ │ │ ├── nobile-webfont.eot │ │ │ ├── nobile-webfont.svg │ │ │ ├── nobile-webfont.ttf │ │ │ ├── nobile-webfont.woff │ │ │ ├── nobile_bold-webfont.eot │ │ │ ├── nobile_bold-webfont.svg │ │ │ ├── nobile_bold-webfont.ttf │ │ │ ├── nobile_bold-webfont.woff │ │ │ ├── nobile_bold_italic-webfont.eot │ │ │ ├── nobile_bold_italic-webfont.svg │ │ │ ├── nobile_bold_italic-webfont.ttf │ │ │ ├── nobile_bold_italic-webfont.woff │ │ │ ├── nobile_italic-webfont.eot │ │ │ ├── nobile_italic-webfont.svg │ │ │ ├── nobile_italic-webfont.ttf │ │ │ ├── nobile_italic-webfont.woff │ │ │ └── stylesheet.css │ │ ├── sample-news-image.png │ │ ├── slides.min.jquery.js │ │ ├── social-buttons.html │ │ ├── transparent.gif │ │ └── unknown.png │ │ └── theme.conf │ ├── about │ ├── difference.rst │ └── index.rst │ ├── citing │ └── index.rst │ ├── conf.py │ ├── documentation │ ├── custom_functions.rst │ ├── debugging.rst │ ├── faq.rst │ ├── functionals.rst │ ├── index.rst │ ├── manual.rst │ ├── maths │ │ ├── 1-foreword.bib │ │ ├── 1-foreword.rst │ │ ├── 2-problem.bib │ │ ├── 2-problem.rst │ │ ├── 3-gradients.bib │ │ ├── 3-gradients.rst │ │ ├── 4-adjoint.bib │ │ ├── 4-adjoint.rst │ │ ├── 5-applications.bib │ │ ├── 5-applications.rst │ │ ├── A-gst.bib │ │ ├── A-gst.rst │ │ └── index.rst │ ├── misc.rst │ ├── optimisation.rst │ ├── parallel.rst │ ├── pyadjoint_api.rst │ ├── pyadjoint_docs.rst │ └── verification.rst │ ├── download │ └── index.rst │ ├── frontpage.rst │ ├── index.rst │ └── support │ └── index.rst ├── examples ├── burgers │ └── burgers.py ├── heat-equation │ └── heat-equation.py ├── klein │ ├── klein.h5 │ ├── klein.py │ ├── klein.xdmf │ └── make-mesh.py ├── mpec │ └── mpec.py ├── poisson-mother │ ├── poisson-mother-ipopt.py │ ├── poisson-mother-rol.py │ ├── poisson-mother-scipy.py │ └── poisson-mother.py ├── poisson-topology │ ├── poisson-topology-3d.py │ └── poisson-topology.py ├── reaction-rate-learning │ ├── concentrations.png │ ├── learned_reaction_rates.png │ ├── navier_stokes_cylinder │ │ ├── compute-flow-field.py │ │ ├── cylinder.xml.gz │ │ └── velocity_series.h5 │ ├── neural_network.py │ └── reaction-rate-learning.py ├── shape-optimization-pipe │ ├── mesh │ │ ├── pipe.geo │ │ ├── pipe.xml │ │ ├── pipe_facet_region.xml │ │ └── pipe_physical_region.xml │ └── shape-optimization-pipe.py ├── stokes-bc-control │ ├── make-mesh.py │ ├── rectangle-less-circle.h5 │ ├── rectangle-less-circle.xdmf │ ├── stokes-bc-control.py │ └── stokes-bc-control_nitsche.py ├── stokes-shape-opt │ ├── create_mesh.py │ ├── mesh.h5 │ ├── mesh.xdmf │ ├── mf.h5 │ ├── mf.xdmf │ └── stokes_problem.py ├── stokes-topology │ ├── stokes-topology-rol-firedrake.py │ ├── stokes-topology-rol.py │ └── stokes-topology.py ├── time-dependent-wave │ └── time-dependent-wave.py ├── time-distributed-control │ └── time-distributed-control.py └── tube-shape-derivative │ ├── mesh │ ├── cable.geo │ ├── cable1.xml │ ├── cable1_facet_region.xml │ ├── cable2.xml │ └── cable2_facet_region.xml │ └── tube-shape-derivative.py ├── joss ├── paper.md └── references.bib ├── numpy_adjoint ├── __init__.py └── array.py ├── pyadjoint ├── __init__.py ├── adjfloat.py ├── block.py ├── block_variable.py ├── checkpointing.py ├── control.py ├── drivers.py ├── enlisting.py ├── ipopt.py ├── optimization │ ├── __init__.py │ ├── constraints.py │ ├── ipopt_solver.py │ ├── moola_problem.py │ ├── optimization.py │ ├── optimization_problem.py │ ├── optimization_solver.py │ ├── rol_solver.py │ └── tao_solver.py ├── ordered_set.py ├── overloaded_function.py ├── overloaded_type.py ├── placeholder.py ├── reduced_functional.py ├── reduced_functional_numpy.py ├── tape.py └── verification.py ├── pyproject.toml ├── setup.cfg └── tests ├── __init__.py ├── conftest.py ├── migration ├── README.md ├── assembled_action │ ├── assembled_action.py │ └── test_assembled_action.py ├── burgers_newton │ ├── burgers_newton.py │ └── test_burgers_newton.py ├── burgers_newton_time_functional │ ├── burgers_newton_time_functional.py │ └── test_burgers_newton_time_functional.py ├── burgers_oo │ ├── burgers_oo.py │ └── test_burgers_oo.py ├── burgers_picard │ ├── burgers_picard.py │ ├── manual_hessian.py │ └── test_burgers_picard.py ├── cahn_hilliard │ ├── cahn_hilliard.py │ ├── paper_adjoint.py │ ├── paper_tlm.py │ ├── test_cahn_hilliard.py │ └── timings │ │ ├── adjoint-2.log │ │ ├── adjoint.log │ │ ├── adjoint.py │ │ ├── annotated-2.log │ │ ├── annotated.log │ │ ├── annotated.py │ │ ├── run_timings.sh │ │ ├── unannotated-2.log │ │ ├── unannotated.log │ │ └── unannotated.py ├── changing_vector │ ├── changing_vector.py │ └── test_changing_vector.py ├── checkpoint_burgers │ ├── checkpoint_burgers.py │ └── test_checkpoint_burgers.py ├── checkpoint_burgers_newton │ ├── checkpoint_burgers_newton.py │ └── test_checkpoint_burgers_newton.py ├── checkpoint_online │ ├── checkpoint_online.py │ └── test_checkpoint_online.py ├── checkpoint_stokes │ ├── checkpoint_stokes.py │ └── test_checkpoint_stokes.py ├── compute_tlm_list_parameter │ ├── compute_tlm_list_parameter.py │ └── test_compute_tlm_list_parameter.py ├── curl-curl │ ├── curl-curl.py │ └── test_curl-curl.py ├── default_parameters │ ├── default_parameters.py │ └── test_default_parameters.py ├── differentiability-dg-upwind │ ├── differentiability-dg-upwind.py │ ├── mesh.xml.gz │ ├── temperature.xml.gz │ ├── test_differentiability-dg-upwind.py │ └── velocity.xml.gz ├── differentiability-stokes │ ├── differentiability-stokes.py │ ├── mesh.xml.gz │ ├── temperature.xml.gz │ ├── test_differentiability-stokes.py │ └── velocity.xml.gz ├── distributed_control │ └── test_distributed_control.py ├── dolfin_adjoint_variable │ ├── dolfin_adjoint_variable.py │ └── test_dolfin_adjoint_variable.py ├── expression_derivative │ ├── expression_derivative.py │ └── test_expression_derivative.py ├── expression_derivative_cpp │ ├── expression_derivative_cpp.py │ └── test_expression_derivative_cpp.py ├── expression_derivative_inline_cpp │ ├── expression_derivative_inline_cpp.py │ └── test_expression_derivative_inline_cpp.py ├── expression_updates │ ├── expression_updates.py │ └── test_expression_updates.py ├── facet_integrals │ └── test_facet_integrals.py ├── fg_constant │ ├── fg_constant.py │ └── test_fg_constant.py ├── fg_constants │ ├── fg_constants.py │ └── test_fg_constants.py ├── function_assign_lincom │ ├── function_assign_lincom.py │ └── test_function_assign_lincom.py ├── function_assigner │ ├── function_assigner.py │ └── test_function_assigner.py ├── function_assigner_givsub │ ├── function_assigner_givsub.py │ └── test_function_assigner_givsub.py ├── functional_dependencies │ ├── functional_dependencies.py │ └── test_functional_dependencies.py ├── functional_form │ ├── functional_form.py │ └── test_functional_form.py ├── functional_operations │ ├── functional_operations.py │ └── test_functional_operations.py ├── functional_value │ ├── functional_value.py │ └── test_functional_value.py ├── gst_mass │ ├── gst_mass.py │ └── test_gst_mass.py ├── heat │ ├── heat.py │ └── test_heat.py ├── hessian_callback │ ├── hessian_callback.py │ └── test_hessian_callback.py ├── hessian_eps │ ├── hessian_eps.py │ └── test_hessian_eps.py ├── hessian_identity │ ├── graph.png │ ├── hessian_identity.py │ ├── manual_hessian.py │ └── test_hessian_identity.py ├── hessian_identity_list │ ├── hessian_identity_list.py │ └── test_hessian_identity_list.py ├── hessian_identity_list2 │ ├── hessian_identity_list2.py │ └── test_hessian_identity_list2.py ├── interpolate │ ├── interpolate.py │ ├── test_interpolate.py │ └── test_interpolate_unit.py ├── krylov_reevaluate │ ├── krylov_reevaluate.py │ └── test_krylov_reevaluate.py ├── linear_solver │ ├── linear_solver.py │ └── test_linear_solver.py ├── list_parameter │ ├── list_parameter.py │ └── test_list_parameter.py ├── localsolver │ ├── localsolver.py │ └── test_localsolver.py ├── localsolver_factorize │ ├── localsolver_factorize.py │ └── test_localsolver_factorize.py ├── lusolver_changing │ ├── lusolver_changing.py │ └── test_lusolver_changing.py ├── lusolver_reassemble │ ├── lusolver_reassemble.py │ └── test_lusolver_reassemble.py ├── lvs │ ├── lvs.py │ └── test_lvs.py ├── manual_hessian │ ├── manual_hessian.py │ └── test_manual_hessian.py ├── matrix_free_burgers │ ├── matrix_free_burgers.py │ └── test_matrix_free_burgers.py ├── matrix_free_heat │ ├── matrix_free_heat.py │ └── test_matrix_free_heat.py ├── matrix_free_simple │ ├── matrix_free_simple.py │ └── test_matrix_free_simple.py ├── matrix_summation │ ├── matrix_summation.py │ └── test_matrix_summation.py ├── mpec │ ├── mpec.py │ ├── test_mpec.py │ └── timing.py ├── multimesh_poisson │ ├── mesh_poisson.py │ ├── multimesh_poisson.py │ └── test_multimesh_poisson.py ├── navier_stokes │ ├── lshape.xml.gz │ ├── navier_stokes.py │ ├── picard.py │ └── test_navier_stokes.py ├── newton_constant │ ├── newton_constant.py │ └── test_newton_constant.py ├── noannotations │ ├── noannotations.py │ └── test_noannotations.py ├── nullspace │ ├── nullspace.py │ └── test_nullspace.py ├── nullspace_linear_solver │ ├── nullspace_linear_solver.py │ └── test_nullspace_linear_solver.py ├── nvs │ ├── nvs.py │ └── test_nvs.py ├── ode_fitzhughnagumo │ ├── basicsinglecellsolver_fitzhughnagumo.py │ ├── fitzhughnagumo.py │ ├── ode_fitzhughnagumo.py │ └── test_ode_fitzhughnagumo.py ├── ode_solver │ ├── ode_solver.py │ └── test_ode_solver.py ├── ode_tentusscher │ ├── ode_tentusscher.py │ ├── tentusscher_2004_mcell.py │ └── test_ode_tentusscher.py ├── ode_tentusscher_quick │ ├── ode_tentusscher_quick.py │ ├── tentusscher_2004_mcell.py │ └── test_ode_tentusscher_quick.py ├── ode_vector │ ├── ode_vector.py │ └── test_ode_vector.py ├── optimal_control_bfgs │ ├── mesh.geo │ ├── mesh.xml │ ├── mesh_physical_region.xml │ ├── optimal_control_bfgs.py │ └── test_optimal_control_bfgs.py ├── optimal_control_mms │ ├── optimal_control_mms.py │ └── test_optimal_control_mms.py ├── optimization_checkpointing │ ├── optimization_checkpointing.py │ └── test_optimization_checkpointing.py ├── optimization_moola │ ├── optimization_moola.py │ └── test_optimization_moola.py ├── optimization_optizelle │ ├── optimization_optizelle.py │ ├── optimization_optizelle_2d.py │ └── test_optimization_optizelle.py ├── optimization_optizelle_algebra │ ├── optimization_optizelle_algebra.py │ └── test_optimization_optizelle_algebra.py ├── optimization_pyipopt │ ├── optimization_pyipopt.py │ └── test_optimization_pyipopt.py ├── optimization_pyopt │ ├── optimization_pyopt.py │ └── test_optimization_pyopt.py ├── optimization_scalar │ ├── optimization_scalar.py │ └── test_optimization_scalar.py ├── optimization_scipy │ ├── optimization_scipy.py │ └── test_optimization_scipy.py ├── optimization_tao │ ├── optimization_tao.py │ └── test_optimization_tao.py ├── periodic │ ├── periodic.py │ └── test_periodic.py ├── petsckrylov_reevaluate │ ├── petsckrylov_reevaluate.py │ └── test_petsckrylov_reevaluate.py ├── picard-linearisation │ ├── picard-linearisation.py │ └── test_picard-linearisation.py ├── pointwise_functional │ ├── pointwise_functional.py │ └── test_pointwise_functional.py ├── pointwise_functional_one_point │ ├── .gitignore │ ├── pointwise_functional_one_point.py │ └── test_pointwise_functional_one_point.py ├── pointwise_functional_regularisation │ ├── .gitignore │ ├── pointwise_functional_regularisation.py │ └── test_pointwise_functional_regularisation.py ├── pointwise_functional_two_points │ ├── .gitignore │ ├── pointwise_functional_two_points.py │ └── test_pointwise_functional_two_points.py ├── pointwise_functional_vector │ ├── pointwise_functional_vector.py │ └── test_pointwise_functional_vector.py ├── preassembly_efficiency │ ├── preassembly_efficiency.py │ └── test_preassembly_efficiency.py ├── projection │ ├── projection.py │ └── test_projection.py ├── reduced_functional │ ├── reduced_functional.py │ └── test_reduced_functional.py ├── reduced_functional_cache │ ├── reduced_functional_cache.py │ └── test_reduced_functional_cache.py ├── reduced_functional_constants │ ├── reduced_functional_constants.py │ └── test_reduced_functional_constants.py ├── reduced_functional_evaluation │ ├── reduced_functional_evaluation.py │ └── test_reduced_functional_evaluation.py ├── rush_larsen │ ├── rush_larsen.py │ └── test_rush_larsen.py ├── shallow_water │ ├── basin.geo │ ├── basin.msh │ ├── basin.xml │ ├── kelvin_new.py │ ├── shallow_water.py │ ├── sw_lib.py │ └── test_shallow_water.py ├── shallow_water_time_functional │ ├── Makefile │ ├── basin.geo │ ├── basin.msh │ ├── basin.xml │ ├── divett.py │ ├── shallow_water_time_functional.py │ ├── sw_lib.py │ └── test_shallow_water_time_functional.py ├── split │ ├── split.py │ └── test_split.py ├── stokes │ ├── stokes.py │ └── test_stokes.py ├── stokes_krylov │ ├── stokes_krylov.py │ └── test_stokes_krylov.py ├── stokes_maday │ ├── stokes_maday.py │ └── test_stokes_maday.py ├── stokes_petsckrylov │ ├── stokes_petsckrylov.py │ └── test_stokes_petsckrylov.py ├── supg │ ├── mesh.xml.gz │ ├── subdomains.xml.gz │ ├── supg.py │ ├── test_supg.py │ └── velocity.xml.gz ├── svd_bc_simple │ ├── svd_bc_simple.py │ └── test_svd_bc_simple.py ├── svd_burgers │ ├── svd_burgers.py │ └── test_svd_burgers.py ├── svd_burgers_perturb │ ├── svd_burgers_perturb.py │ └── test_svd_burgers_perturb.py ├── svd_simple │ ├── svd_simple.py │ └── test_svd_simple.py ├── taylor_hessian │ ├── taylor_hessian.py │ └── test_taylor_hessian.py ├── time_dependent_data │ ├── test_time_dependent_data.py │ └── time_dependent_data.py ├── time_functionals │ ├── test_time_functionals.py │ └── time_functionals.py ├── time_functionals_no_annotation │ ├── test_time_functionals_no_annotation.py │ └── time_functionals_no_annotation.py ├── timeforms │ └── test_timeforms.py ├── tlm_burgers │ ├── test_tlm_burgers.py │ └── tlm_burgers.py ├── tlm_list_parameter │ ├── test_tlm_list_parameter.py │ └── tlm_list_parameter.py ├── tlm_scalar_parameter │ ├── test_tlm_scalar_parameter.py │ └── tlm_scalar_parameter.py ├── tlm_simple │ ├── test_tlm_simple.py │ └── tlm_simple.py ├── upwind │ ├── mesh.xml.gz │ ├── test_upwind.py │ ├── upwind.py │ └── velocity.xml.gz ├── 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