diff --git a/.github/workflows/lychee_url_checker.yml b/.github/workflows/lychee_url_checker.yml index e99ba9c290..d9ab150ded 100644 --- a/.github/workflows/lychee_url_checker.yml +++ b/.github/workflows/lychee_url_checker.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest steps: - # cache Lychee results to avoid hitting rate limits + # cache Lychee results to avoid hitting rate limits - name: Restore lychee cache uses: actions/cache@v3 with: @@ -42,7 +42,7 @@ jobs: --exclude https://twitter.com/pybamm_ --exclude "https://doi\.org|www.sciencedirect\.com/*" --accept 200,429 - --exclude-path ./CHANGELOG.md + --exclude-path ./CHANGELOG.md --exclude-path ./scripts/update_version.py './**/*.rst' './**/*.md' diff --git a/.github/workflows/need_reply_remove.yml b/.github/workflows/need_reply_remove.yml index 59f9a839ed..4ce8ae81f4 100644 --- a/.github/workflows/need_reply_remove.yml +++ b/.github/workflows/need_reply_remove.yml @@ -22,4 +22,4 @@ jobs: issue: ${{ github.event.issue.number }} label: needs-reply env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/needs_reply.yml b/.github/workflows/needs_reply.yml index 8e9269001b..7dde7bfef6 100644 --- a/.github/workflows/needs_reply.yml +++ b/.github/workflows/needs_reply.yml @@ -13,4 +13,4 @@ jobs: uses: dwieeb/needs-reply@v2 with: repo-token: ${{ secrets.GITHUB_TOKEN }} - issue-label: needs-reply \ No newline at end of file + issue-label: needs-reply diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml index 41e4a9de8a..5027d877ac 100644 --- a/.github/workflows/run_periodic_tests.yml +++ b/.github/workflows/run_periodic_tests.yml @@ -1,11 +1,11 @@ -# Run all unit tests and integration tests for all Python versions +# Run all unit tests and integration tests for all Python versions # and platforms at 3am UTC every day and on PRs to the main branch name: Scheduled on: workflow_dispatch: pull_request: - branches: + branches: - main # Run everyday at 3 am UTC @@ -119,13 +119,13 @@ jobs: build-apple-mseries: needs: style runs-on: [self-hosted, macOS, ARM64] - env: + env: GITHUB_PATH: ${PYENV_ROOT/bin:$PATH} strategy: fail-fast: false matrix: python-version: ["3.8", "3.9", "3.10", "3.11"] - + steps: - uses: actions/checkout@v3 - name: Install python & create virtualenv diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 88e655c09a..964b9c30eb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -40,4 +40,4 @@ repos: - id: python-check-blanket-type-ignore - id: rst-backticks - id: rst-directive-colons - - id: rst-inline-touching-normal \ No newline at end of file + - id: rst-inline-touching-normal diff --git a/CMakeLists.txt b/CMakeLists.txt index cc47ba99c0..c3c5141d4f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -34,7 +34,7 @@ if(NOT PYBIND11_DIR) endif() add_subdirectory(${PYBIND11_DIR}) -pybind11_add_module(idaklu +pybind11_add_module(idaklu pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp pybamm/solvers/c_solvers/idaklu/casadi_functions.hpp pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp @@ -56,7 +56,7 @@ if (NOT DEFINED USE_PYTHON_CASADI) endif() execute_process( - COMMAND "${PYTHON_EXECUTABLE}" -c + COMMAND "${PYTHON_EXECUTABLE}" -c "import casadi as _; print(_.__path__[0])" OUTPUT_VARIABLE CASADI_DIR OUTPUT_STRIP_TRAILING_WHITESPACE) @@ -67,7 +67,7 @@ endif() message("Found python casadi path: ${CASADI_DIR}") if(${USE_PYTHON_CASADI}) - message("Trying to link against python casadi package") + message("Trying to link against python casadi package") find_package(casadi CONFIG PATHS ${CASADI_DIR} REQUIRED) else() message("Trying to link against any casadi package apart from the python one") @@ -78,7 +78,7 @@ endif() set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}) # Sundials find_package(SUNDIALS REQUIRED) -message("sundials ${SUNDIALS_INCLUDE_DIR} ${SUNDIALS_LIBRARIES}") +message("sundials ${SUNDIALS_INCLUDE_DIR} ${SUNDIALS_LIBRARIES}") target_include_directories(idaklu PRIVATE ${SUNDIALS_INCLUDE_DIR}) target_link_libraries(idaklu PRIVATE ${SUNDIALS_LIBRARIES} casadi) diff --git a/FindSuiteSparse.cmake b/FindSuiteSparse.cmake index 532007e7ae..c5275c02c0 100644 --- a/FindSuiteSparse.cmake +++ b/FindSuiteSparse.cmake @@ -1,4 +1,4 @@ -# This CMakeFile is adapted from that in dune-common: +# This CMakeFile is adapted from that in dune-common: # .. cmake_module:: # @@ -239,4 +239,3 @@ endif() #set HAVE_SUITESPARSE for config.h set(HAVE_SUITESPARSE ${SuiteSparse_FOUND}) set(HAVE_UMFPACK ${SuiteSparse_UMFPACK_FOUND}) - diff --git a/README.md b/README.md index 04070f0d4a..acc7157cb7 100644 --- a/README.md +++ b/README.md @@ -41,8 +41,8 @@ pay for developer time, professional services, travel, workshops, and a variety
-
diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py index 8b13789179..e69de29bb2 100644 --- a/benchmarks/__init__.py +++ b/benchmarks/__init__.py @@ -1 +0,0 @@ - diff --git a/build_manylinux_wheels/Dockerfile b/build_manylinux_wheels/Dockerfile index efaef13a1f..a6c2dcc41c 100644 --- a/build_manylinux_wheels/Dockerfile +++ b/build_manylinux_wheels/Dockerfile @@ -15,4 +15,4 @@ RUN chmod +x /entrypoint.sh RUN ./install_sundials.sh -ENTRYPOINT ["/entrypoint.sh"] \ No newline at end of file +ENTRYPOINT ["/entrypoint.sh"] diff --git a/build_manylinux_wheels/install_sundials.sh b/build_manylinux_wheels/install_sundials.sh index e97817a367..709d9c13c7 100644 --- a/build_manylinux_wheels/install_sundials.sh +++ b/build_manylinux_wheels/install_sundials.sh @@ -78,4 +78,3 @@ cmake -DENABLE_LAPACK=ON\ -DCMAKE_INSTALL_PREFIX=/usr\ ../$SUNDIALS_DIR make install - diff --git a/docs/Makefile b/docs/Makefile index b454275837..46d9ea6f19 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -17,4 +17,3 @@ help: # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - diff --git a/docs/_static/index-images/api.svg b/docs/_static/index-images/api.svg index e637525cc0..2cbc9a9403 100644 --- a/docs/_static/index-images/api.svg +++ b/docs/_static/index-images/api.svg @@ -5,27 +5,27 @@ - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/_static/index-images/contributor.svg b/docs/_static/index-images/contributor.svg index 3a689e0e4c..b03a9a2b19 100644 --- a/docs/_static/index-images/contributor.svg +++ b/docs/_static/index-images/contributor.svg @@ -1 +1 @@ - \ No newline at end of file + diff --git a/docs/_static/index-images/examples.svg b/docs/_static/index-images/examples.svg index d61b0937da..a8057b819b 100644 --- a/docs/_static/index-images/examples.svg +++ b/docs/_static/index-images/examples.svg @@ -1 +1 @@ - \ No newline at end of file + diff --git a/docs/_static/index-images/getting_started.svg b/docs/_static/index-images/getting_started.svg index 04db7e6156..463ef73e34 100644 --- a/docs/_static/index-images/getting_started.svg +++ b/docs/_static/index-images/getting_started.svg @@ -5,27 +5,27 @@ - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/conf.py b/docs/conf.py index 43f71f704e..336fa15743 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -314,7 +314,7 @@

An interactive online version of this notebook is available, which can be accessed via - Open this notebook in Google Colab diff --git a/docs/index.rst b/docs/index.rst index 21b224a331..3e5d54ecb5 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -28,7 +28,7 @@ PyBaMM documentation PyBaMM (Python Battery Mathematical Modelling) is an open-source battery simulation package written in Python. Our mission is to accelerate battery modelling research by -providing open-source tools for multi-institutional, interdisciplinary collaboration. +providing open-source tools for multi-institutional, interdisciplinary collaboration. Broadly, PyBaMM consists of #. a framework for writing and solving systems of differential equations, @@ -57,7 +57,7 @@ explore the effect of different battery designs and modeling assumptions under a :click-parent: To the user guide - + .. grid-item-card:: :img-top: _static/index-images/examples.svg diff --git a/docs/source/api/batch_study.rst b/docs/source/api/batch_study.rst index f00a2b1657..51e927d856 100644 --- a/docs/source/api/batch_study.rst +++ b/docs/source/api/batch_study.rst @@ -2,4 +2,4 @@ Batch Study =========== .. autoclass:: pybamm.BatchStudy - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/experiment/experiment_steps.rst b/docs/source/api/experiment/experiment_steps.rst index a4637a866b..55de9d17bf 100644 --- a/docs/source/api/experiment/experiment_steps.rst +++ b/docs/source/api/experiment/experiment_steps.rst @@ -17,4 +17,4 @@ These functions return the following step class, which is not intended to be use directly: .. autoclass:: pybamm.step._Step - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/expression_tree/array.rst b/docs/source/api/expression_tree/array.rst index a84a856a19..7b398ea8e7 100644 --- a/docs/source/api/expression_tree/array.rst +++ b/docs/source/api/expression_tree/array.rst @@ -6,4 +6,4 @@ Array .. autofunction:: pybamm.linspace -.. autofunction:: pybamm.meshgrid +.. autofunction:: pybamm.meshgrid diff --git a/docs/source/api/expression_tree/matrix.rst b/docs/source/api/expression_tree/matrix.rst index 71a281bd8a..c07c9c4462 100644 --- a/docs/source/api/expression_tree/matrix.rst +++ b/docs/source/api/expression_tree/matrix.rst @@ -3,4 +3,3 @@ Matrix .. autoclass:: pybamm.Matrix :members: - diff --git a/docs/source/api/expression_tree/operations/evaluate.rst b/docs/source/api/expression_tree/operations/evaluate.rst index ab3e9e14f2..6429c1f370 100644 --- a/docs/source/api/expression_tree/operations/evaluate.rst +++ b/docs/source/api/expression_tree/operations/evaluate.rst @@ -1,6 +1,5 @@ -EvaluatorPython +EvaluatorPython =============== .. autoclass:: pybamm.EvaluatorPython :members: - diff --git a/docs/source/api/expression_tree/scalar.rst b/docs/source/api/expression_tree/scalar.rst index e02ee39bf8..ca5ea1aae3 100644 --- a/docs/source/api/expression_tree/scalar.rst +++ b/docs/source/api/expression_tree/scalar.rst @@ -3,4 +3,3 @@ Scalar .. autoclass:: pybamm.Scalar :members: - diff --git a/docs/source/api/expression_tree/symbol.rst b/docs/source/api/expression_tree/symbol.rst index be252c9b06..41f390e1ac 100644 --- a/docs/source/api/expression_tree/symbol.rst +++ b/docs/source/api/expression_tree/symbol.rst @@ -5,4 +5,3 @@ Symbol .. autoclass:: pybamm.Symbol :special-members: :members: - diff --git a/docs/source/api/expression_tree/variable.rst b/docs/source/api/expression_tree/variable.rst index ab42f76bcf..8028ceaf56 100644 --- a/docs/source/api/expression_tree/variable.rst +++ b/docs/source/api/expression_tree/variable.rst @@ -6,4 +6,3 @@ Variable .. autoclass:: pybamm.VariableDot :members: - diff --git a/docs/source/api/geometry/index.rst b/docs/source/api/geometry/index.rst index b63b5ce82c..0dd5fc294c 100644 --- a/docs/source/api/geometry/index.rst +++ b/docs/source/api/geometry/index.rst @@ -5,4 +5,3 @@ Geometry geometry battery_geometry - diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst index 34c888339d..432461a58e 100644 --- a/docs/source/api/index.rst +++ b/docs/source/api/index.rst @@ -29,4 +29,4 @@ For a high-level introduction to PyBaMM, see the :ref:`user guide ` util callbacks citations - batch_study \ No newline at end of file + batch_study diff --git a/docs/source/api/meshes/meshes.rst b/docs/source/api/meshes/meshes.rst index 671839c278..db96c58f00 100644 --- a/docs/source/api/meshes/meshes.rst +++ b/docs/source/api/meshes/meshes.rst @@ -6,6 +6,6 @@ Meshes .. autoclass:: pybamm.SubMesh :members: - + .. autoclass:: pybamm.MeshGenerator :members: diff --git a/docs/source/api/models/base_models/base_battery_model.rst b/docs/source/api/models/base_models/base_battery_model.rst index 64715ae5d4..1ce24ebdeb 100644 --- a/docs/source/api/models/base_models/base_battery_model.rst +++ b/docs/source/api/models/base_models/base_battery_model.rst @@ -7,4 +7,4 @@ Base Battery Model :members: .. autoclass:: pybamm.BatteryModelOptions - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/base_models/event.rst b/docs/source/api/models/base_models/event.rst index 856fb2b68f..daf873f898 100644 --- a/docs/source/api/models/base_models/event.rst +++ b/docs/source/api/models/base_models/event.rst @@ -6,5 +6,3 @@ Event .. autoclass:: pybamm.EventType :members: - - diff --git a/docs/source/api/models/index.rst b/docs/source/api/models/index.rst index e62d4a2beb..a259e3cb7f 100644 --- a/docs/source/api/models/index.rst +++ b/docs/source/api/models/index.rst @@ -4,7 +4,7 @@ Models Below is an overview of all the battery models included in PyBaMM. Each of the pre-built models contains a reference to the paper in which it is derived. -The models can be customised using the `options` dictionary defined in the :class:`pybamm.BaseBatteryModel` (which also provides information on which options and models are compatible) +The models can be customised using the ``options`` dictionary defined in the :class:`pybamm.BaseBatteryModel` (which also provides information on which options and models are compatible) Visit our `examples page `_ to see how these models can be solved, and compared, using PyBaMM. diff --git a/docs/source/api/models/lead_acid/full.rst b/docs/source/api/models/lead_acid/full.rst index a07a38949f..4cc6af7cc0 100644 --- a/docs/source/api/models/lead_acid/full.rst +++ b/docs/source/api/models/lead_acid/full.rst @@ -7,4 +7,4 @@ Full Model .. autoclass:: pybamm.lead_acid.BasicFull :members: -.. footbibliography:: \ No newline at end of file +.. footbibliography:: diff --git a/docs/source/api/models/lithium_ion/index.rst b/docs/source/api/models/lithium_ion/index.rst index 8148824dd9..f925d2c3d4 100644 --- a/docs/source/api/models/lithium_ion/index.rst +++ b/docs/source/api/models/lithium_ion/index.rst @@ -10,4 +10,4 @@ Lithium-ion Models dfn newman_tobias yang2017 - electrode_soh \ No newline at end of file + electrode_soh diff --git a/docs/source/api/models/lithium_ion/yang2017.rst b/docs/source/api/models/lithium_ion/yang2017.rst index 06134be58d..1ee5bad80d 100644 --- a/docs/source/api/models/lithium_ion/yang2017.rst +++ b/docs/source/api/models/lithium_ion/yang2017.rst @@ -3,4 +3,3 @@ Yang et al 2017 .. autoclass:: pybamm.lithium_ion.Yang2017 :members: - diff --git a/docs/source/api/models/submodels/active_material/base_active_material.rst b/docs/source/api/models/submodels/active_material/base_active_material.rst index 6eab5fe0a0..f94c816d51 100644 --- a/docs/source/api/models/submodels/active_material/base_active_material.rst +++ b/docs/source/api/models/submodels/active_material/base_active_material.rst @@ -3,4 +3,3 @@ Base Model .. autoclass:: pybamm.active_material.BaseModel :members: - diff --git a/docs/source/api/models/submodels/active_material/constant_active_material.rst b/docs/source/api/models/submodels/active_material/constant_active_material.rst index 9102c533d2..2d022563cb 100644 --- a/docs/source/api/models/submodels/active_material/constant_active_material.rst +++ b/docs/source/api/models/submodels/active_material/constant_active_material.rst @@ -3,5 +3,3 @@ Constant Active Material .. autoclass:: pybamm.active_material.Constant :members: - - diff --git a/docs/source/api/models/submodels/active_material/index.rst b/docs/source/api/models/submodels/active_material/index.rst index 1022c9c6c0..ed075940c5 100644 --- a/docs/source/api/models/submodels/active_material/index.rst +++ b/docs/source/api/models/submodels/active_material/index.rst @@ -9,4 +9,3 @@ Submodels for (loss of) active material base_active_material constant_active_material loss_active_material - diff --git a/docs/source/api/models/submodels/active_material/loss_active_material.rst b/docs/source/api/models/submodels/active_material/loss_active_material.rst index 37072847a1..e600806a1c 100644 --- a/docs/source/api/models/submodels/active_material/loss_active_material.rst +++ b/docs/source/api/models/submodels/active_material/loss_active_material.rst @@ -1,4 +1,4 @@ -Loss of Active Material +Loss of Active Material ======================= .. autoclass:: pybamm.active_material.LossActiveMaterial diff --git a/docs/source/api/models/submodels/base_submodel.rst b/docs/source/api/models/submodels/base_submodel.rst index a407963142..41a2c178b0 100644 --- a/docs/source/api/models/submodels/base_submodel.rst +++ b/docs/source/api/models/submodels/base_submodel.rst @@ -3,4 +3,3 @@ Base Submodel .. autoclass:: pybamm.BaseSubModel :members: - diff --git a/docs/source/api/models/submodels/electrode/ohm/index.rst b/docs/source/api/models/submodels/electrode/ohm/index.rst index 63b4727fe0..ad4a16ff2c 100644 --- a/docs/source/api/models/submodels/electrode/ohm/index.rst +++ b/docs/source/api/models/submodels/electrode/ohm/index.rst @@ -8,4 +8,4 @@ Ohmic composite_ohm full_ohm surface_form_ohm - li_metal_explicit \ No newline at end of file + li_metal_explicit diff --git a/docs/source/api/models/submodels/electrolyte_conductivity/base_electrolyte_conductivity.rst b/docs/source/api/models/submodels/electrolyte_conductivity/base_electrolyte_conductivity.rst index 4a2fb4d0b1..ca6cc18095 100644 --- a/docs/source/api/models/submodels/electrolyte_conductivity/base_electrolyte_conductivity.rst +++ b/docs/source/api/models/submodels/electrolyte_conductivity/base_electrolyte_conductivity.rst @@ -3,4 +3,3 @@ Base Electrolyte Conductivity Submodel .. autoclass:: pybamm.electrolyte_conductivity.BaseElectrolyteConductivity :members: - diff --git a/docs/source/api/models/submodels/electrolyte_conductivity/full_conductivity.rst b/docs/source/api/models/submodels/electrolyte_conductivity/full_conductivity.rst index 6882fbb8e2..017811f313 100644 --- a/docs/source/api/models/submodels/electrolyte_conductivity/full_conductivity.rst +++ b/docs/source/api/models/submodels/electrolyte_conductivity/full_conductivity.rst @@ -4,4 +4,3 @@ Full Model .. autoclass:: pybamm.electrolyte_conductivity.Full :members: :inherited-members: - diff --git a/docs/source/api/models/submodels/electrolyte_conductivity/leading_order_conductivity.rst b/docs/source/api/models/submodels/electrolyte_conductivity/leading_order_conductivity.rst index e5e6f0261c..31a91b8498 100644 --- a/docs/source/api/models/submodels/electrolyte_conductivity/leading_order_conductivity.rst +++ b/docs/source/api/models/submodels/electrolyte_conductivity/leading_order_conductivity.rst @@ -3,4 +3,3 @@ Leading Order Model .. autoclass:: pybamm.electrolyte_conductivity.LeadingOrder :members: - diff --git a/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/index.rst b/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/index.rst index de0c5b1fd1..bb49e378e6 100644 --- a/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/index.rst +++ b/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/index.rst @@ -5,4 +5,4 @@ Surface Form full_surface_form_conductivity leading_surface_form_conductivity - explicit_surface_form_conductivity \ No newline at end of file + explicit_surface_form_conductivity diff --git a/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/leading_surface_form_conductivity.rst b/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/leading_surface_form_conductivity.rst index 07154f9aa6..0a5b7c2756 100644 --- a/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/leading_surface_form_conductivity.rst +++ b/docs/source/api/models/submodels/electrolyte_conductivity/surface_form/leading_surface_form_conductivity.rst @@ -3,6 +3,6 @@ Leading Order Model .. autoclass:: pybamm.electrolyte_conductivity.surface_potential_form.LeadingOrderDifferential :members: - + .. autoclass:: pybamm.electrolyte_conductivity.surface_potential_form.LeadingOrderAlgebraic :members: diff --git a/docs/source/api/models/submodels/electrolyte_diffusion/constant_concentration.rst b/docs/source/api/models/submodels/electrolyte_diffusion/constant_concentration.rst index be326a8f6d..7d5109d974 100644 --- a/docs/source/api/models/submodels/electrolyte_diffusion/constant_concentration.rst +++ b/docs/source/api/models/submodels/electrolyte_diffusion/constant_concentration.rst @@ -3,4 +3,3 @@ Constant Concentration .. autoclass:: pybamm.electrolyte_diffusion.ConstantConcentration :members: - diff --git a/docs/source/api/models/submodels/electrolyte_diffusion/full_diffusion.rst b/docs/source/api/models/submodels/electrolyte_diffusion/full_diffusion.rst index 99dd1fee93..cbf6da93d4 100644 --- a/docs/source/api/models/submodels/electrolyte_diffusion/full_diffusion.rst +++ b/docs/source/api/models/submodels/electrolyte_diffusion/full_diffusion.rst @@ -3,4 +3,3 @@ Full Model .. autoclass:: pybamm.electrolyte_diffusion.Full :members: - diff --git a/docs/source/api/models/submodels/electrolyte_diffusion/leading_order_diffusion.rst b/docs/source/api/models/submodels/electrolyte_diffusion/leading_order_diffusion.rst index a4c817c60d..4005165095 100644 --- a/docs/source/api/models/submodels/electrolyte_diffusion/leading_order_diffusion.rst +++ b/docs/source/api/models/submodels/electrolyte_diffusion/leading_order_diffusion.rst @@ -3,5 +3,3 @@ Leading Order Model .. autoclass:: pybamm.electrolyte_diffusion.LeadingOrder :members: - - diff --git a/docs/source/api/models/submodels/equivalent_circuit_elements/ocv_element.rst b/docs/source/api/models/submodels/equivalent_circuit_elements/ocv_element.rst index f34a563edc..025e40eb92 100644 --- a/docs/source/api/models/submodels/equivalent_circuit_elements/ocv_element.rst +++ b/docs/source/api/models/submodels/equivalent_circuit_elements/ocv_element.rst @@ -3,4 +3,3 @@ OCV Element .. autoclass:: pybamm.equivalent_circuit_elements.OCVElement :members: - diff --git a/docs/source/api/models/submodels/equivalent_circuit_elements/rc_element.rst b/docs/source/api/models/submodels/equivalent_circuit_elements/rc_element.rst index e783f4b291..bc938e4619 100644 --- a/docs/source/api/models/submodels/equivalent_circuit_elements/rc_element.rst +++ b/docs/source/api/models/submodels/equivalent_circuit_elements/rc_element.rst @@ -3,4 +3,3 @@ RC Element .. autoclass:: pybamm.equivalent_circuit_elements.RCElement :members: - diff --git a/docs/source/api/models/submodels/equivalent_circuit_elements/resistor_element.rst b/docs/source/api/models/submodels/equivalent_circuit_elements/resistor_element.rst index 91d6e6d2c5..d519db70bf 100644 --- a/docs/source/api/models/submodels/equivalent_circuit_elements/resistor_element.rst +++ b/docs/source/api/models/submodels/equivalent_circuit_elements/resistor_element.rst @@ -3,4 +3,3 @@ Resistor Element .. autoclass:: pybamm.equivalent_circuit_elements.ResistorElement :members: - diff --git a/docs/source/api/models/submodels/equivalent_circuit_elements/thermal.rst b/docs/source/api/models/submodels/equivalent_circuit_elements/thermal.rst index c95ead818f..a3c3ac62a7 100644 --- a/docs/source/api/models/submodels/equivalent_circuit_elements/thermal.rst +++ b/docs/source/api/models/submodels/equivalent_circuit_elements/thermal.rst @@ -3,4 +3,3 @@ Thermal SubModel .. autoclass:: pybamm.equivalent_circuit_elements.ThermalSubModel :members: - diff --git a/docs/source/api/models/submodels/equivalent_circuit_elements/voltage_model.rst b/docs/source/api/models/submodels/equivalent_circuit_elements/voltage_model.rst index bda725dfcb..caa08f188f 100644 --- a/docs/source/api/models/submodels/equivalent_circuit_elements/voltage_model.rst +++ b/docs/source/api/models/submodels/equivalent_circuit_elements/voltage_model.rst @@ -3,4 +3,3 @@ Voltage Model .. autoclass:: pybamm.equivalent_circuit_elements.VoltageModel :members: - diff --git a/docs/source/api/models/submodels/external_circuit/function_control_external_circuit.rst b/docs/source/api/models/submodels/external_circuit/function_control_external_circuit.rst index e977600663..baa9454076 100644 --- a/docs/source/api/models/submodels/external_circuit/function_control_external_circuit.rst +++ b/docs/source/api/models/submodels/external_circuit/function_control_external_circuit.rst @@ -14,4 +14,4 @@ Function control external circuit :members: .. autoclass:: pybamm.external_circuit.CCCVFunctionControl - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/base_kinetics.rst b/docs/source/api/models/submodels/interface/kinetics/base_kinetics.rst index 67e4f15cf0..b17fb73a4d 100644 --- a/docs/source/api/models/submodels/interface/kinetics/base_kinetics.rst +++ b/docs/source/api/models/submodels/interface/kinetics/base_kinetics.rst @@ -2,4 +2,4 @@ Base Kinetics ============= .. autoclass:: pybamm.kinetics.BaseKinetics - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/butler_volmer.rst b/docs/source/api/models/submodels/interface/kinetics/butler_volmer.rst index 0c46b217c5..abf878e57b 100644 --- a/docs/source/api/models/submodels/interface/kinetics/butler_volmer.rst +++ b/docs/source/api/models/submodels/interface/kinetics/butler_volmer.rst @@ -5,4 +5,4 @@ Butler Volumer :members: .. autoclass:: pybamm.kinetics.AsymmetricButlerVolmer - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/index.rst b/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/index.rst index 260259ad3d..f6d3f495ff 100644 --- a/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/index.rst +++ b/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/index.rst @@ -3,4 +3,4 @@ Inverse Kinetics .. toctree:: - inverse_butler_volmer \ No newline at end of file + inverse_butler_volmer diff --git a/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/inverse_butler_volmer.rst b/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/inverse_butler_volmer.rst index 3a2f7e3e3b..60bd3c7c0d 100644 --- a/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/inverse_butler_volmer.rst +++ b/docs/source/api/models/submodels/interface/kinetics/inverse_kinetics/inverse_butler_volmer.rst @@ -2,4 +2,4 @@ Inverse Butler-Volmer ===================== .. autoclass:: pybamm.kinetics.InverseButlerVolmer - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/linear.rst b/docs/source/api/models/submodels/interface/kinetics/linear.rst index 57bc5b5437..22c02cbe21 100644 --- a/docs/source/api/models/submodels/interface/kinetics/linear.rst +++ b/docs/source/api/models/submodels/interface/kinetics/linear.rst @@ -2,4 +2,4 @@ Linear ====== .. autoclass:: pybamm.kinetics.Linear - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/marcus.rst b/docs/source/api/models/submodels/interface/kinetics/marcus.rst index 2c72b71e5d..6252f22e8b 100644 --- a/docs/source/api/models/submodels/interface/kinetics/marcus.rst +++ b/docs/source/api/models/submodels/interface/kinetics/marcus.rst @@ -2,4 +2,4 @@ Marcus ====== .. autoclass:: pybamm.kinetics.Marcus - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/no_reaction.rst b/docs/source/api/models/submodels/interface/kinetics/no_reaction.rst index 4da4e490a9..573b9a2117 100644 --- a/docs/source/api/models/submodels/interface/kinetics/no_reaction.rst +++ b/docs/source/api/models/submodels/interface/kinetics/no_reaction.rst @@ -2,4 +2,4 @@ NoReaction ========== .. autoclass:: pybamm.kinetics.NoReaction - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/tafel.rst b/docs/source/api/models/submodels/interface/kinetics/tafel.rst index 23280eea8a..1969ab5b53 100644 --- a/docs/source/api/models/submodels/interface/kinetics/tafel.rst +++ b/docs/source/api/models/submodels/interface/kinetics/tafel.rst @@ -2,4 +2,4 @@ Tafel ===== .. autoclass:: pybamm.kinetics.ForwardTafel - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/kinetics/total_main_kinetics.rst b/docs/source/api/models/submodels/interface/kinetics/total_main_kinetics.rst index b8462437d2..36b17e2564 100644 --- a/docs/source/api/models/submodels/interface/kinetics/total_main_kinetics.rst +++ b/docs/source/api/models/submodels/interface/kinetics/total_main_kinetics.rst @@ -3,4 +3,4 @@ Total Main Kinetics .. autoclass:: pybamm.kinetics.TotalMainKinetics - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/lithium_plating/index.rst b/docs/source/api/models/submodels/interface/lithium_plating/index.rst index 3edc2652d2..29bca51941 100644 --- a/docs/source/api/models/submodels/interface/lithium_plating/index.rst +++ b/docs/source/api/models/submodels/interface/lithium_plating/index.rst @@ -5,4 +5,4 @@ Lithium Plating base_plating no_plating - plating \ No newline at end of file + plating diff --git a/docs/source/api/models/submodels/interface/open_circuit_potential/base_ocp.rst b/docs/source/api/models/submodels/interface/open_circuit_potential/base_ocp.rst index e06196b6a8..41b0fdbb28 100644 --- a/docs/source/api/models/submodels/interface/open_circuit_potential/base_ocp.rst +++ b/docs/source/api/models/submodels/interface/open_circuit_potential/base_ocp.rst @@ -2,4 +2,4 @@ Base Open Circuit Potential =========================== .. autoclass:: pybamm.open_circuit_potential.BaseOpenCircuitPotential - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/open_circuit_potential/current_sigmoid_ocp.rst b/docs/source/api/models/submodels/interface/open_circuit_potential/current_sigmoid_ocp.rst index f71e360495..832cc57603 100644 --- a/docs/source/api/models/submodels/interface/open_circuit_potential/current_sigmoid_ocp.rst +++ b/docs/source/api/models/submodels/interface/open_circuit_potential/current_sigmoid_ocp.rst @@ -3,4 +3,3 @@ Current Sigmoid Open Circuit Potential .. autoclass:: pybamm.open_circuit_potential.CurrentSigmoidOpenCircuitPotential :members: - diff --git a/docs/source/api/models/submodels/interface/sei/base_sei.rst b/docs/source/api/models/submodels/interface/sei/base_sei.rst index bcfad871da..2e42e0eea9 100644 --- a/docs/source/api/models/submodels/interface/sei/base_sei.rst +++ b/docs/source/api/models/submodels/interface/sei/base_sei.rst @@ -2,4 +2,4 @@ SEI Base Model ============== .. autoclass:: pybamm.sei.BaseModel - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/sei/constant_sei.rst b/docs/source/api/models/submodels/interface/sei/constant_sei.rst index e92180d1ca..a38652daa8 100644 --- a/docs/source/api/models/submodels/interface/sei/constant_sei.rst +++ b/docs/source/api/models/submodels/interface/sei/constant_sei.rst @@ -2,4 +2,4 @@ Constant SEI ============ .. autoclass:: pybamm.sei.ConstantSEI - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/sei/index.rst b/docs/source/api/models/submodels/interface/sei/index.rst index 07ecc475e3..3468f2d0ef 100644 --- a/docs/source/api/models/submodels/interface/sei/index.rst +++ b/docs/source/api/models/submodels/interface/sei/index.rst @@ -7,4 +7,4 @@ SEI models constant_sei no_sei sei_growth - total_sei \ No newline at end of file + total_sei diff --git a/docs/source/api/models/submodels/interface/sei/no_sei.rst b/docs/source/api/models/submodels/interface/sei/no_sei.rst index dde5f645fe..69e93f5d2e 100644 --- a/docs/source/api/models/submodels/interface/sei/no_sei.rst +++ b/docs/source/api/models/submodels/interface/sei/no_sei.rst @@ -2,4 +2,4 @@ No SEI ====== .. autoclass:: pybamm.sei.NoSEI - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/interface/sei/total_sei.rst b/docs/source/api/models/submodels/interface/sei/total_sei.rst index 7f65c9cae3..4210bcd47f 100644 --- a/docs/source/api/models/submodels/interface/sei/total_sei.rst +++ b/docs/source/api/models/submodels/interface/sei/total_sei.rst @@ -2,4 +2,4 @@ Total SEI ========= .. autoclass:: pybamm.sei.TotalSEI - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/models/submodels/particle/index.rst b/docs/source/api/models/submodels/particle/index.rst index a701eeec6e..ae020ac3fa 100644 --- a/docs/source/api/models/submodels/particle/index.rst +++ b/docs/source/api/models/submodels/particle/index.rst @@ -7,4 +7,4 @@ Particle base_particle fickian_diffusion polynomial_profile - x_averaged_polynomial_profile \ No newline at end of file + x_averaged_polynomial_profile diff --git a/docs/source/api/models/submodels/porosity/base_porosity.rst b/docs/source/api/models/submodels/porosity/base_porosity.rst index 0886e2502c..a328047f4c 100644 --- a/docs/source/api/models/submodels/porosity/base_porosity.rst +++ b/docs/source/api/models/submodels/porosity/base_porosity.rst @@ -3,4 +3,3 @@ Base Model .. autoclass:: pybamm.porosity.BaseModel :members: - diff --git a/docs/source/api/models/submodels/porosity/constant_porosity.rst b/docs/source/api/models/submodels/porosity/constant_porosity.rst index babb63bd36..7eff146917 100644 --- a/docs/source/api/models/submodels/porosity/constant_porosity.rst +++ b/docs/source/api/models/submodels/porosity/constant_porosity.rst @@ -1,7 +1,5 @@ -Constant Porosity +Constant Porosity ================= .. autoclass:: pybamm.porosity.Constant :members: - - diff --git a/docs/source/api/models/submodels/porosity/index.rst b/docs/source/api/models/submodels/porosity/index.rst index deadc9e5c5..17d0f23fb8 100644 --- a/docs/source/api/models/submodels/porosity/index.rst +++ b/docs/source/api/models/submodels/porosity/index.rst @@ -8,4 +8,3 @@ Porosity constant_porosity reaction_driven_porosity reaction_driven_porosity_ode - diff --git a/docs/source/api/models/submodels/porosity/reaction_driven_porosity.rst b/docs/source/api/models/submodels/porosity/reaction_driven_porosity.rst index dc4dfc8d42..35d77d20d9 100644 --- a/docs/source/api/models/submodels/porosity/reaction_driven_porosity.rst +++ b/docs/source/api/models/submodels/porosity/reaction_driven_porosity.rst @@ -1,8 +1,5 @@ -Reaction-driven Model +Reaction-driven Model ===================== .. autoclass:: pybamm.porosity.ReactionDriven :members: - - - diff --git a/docs/source/api/models/submodels/porosity/reaction_driven_porosity_ode.rst b/docs/source/api/models/submodels/porosity/reaction_driven_porosity_ode.rst index f74f7d5c30..afa0e5f358 100644 --- a/docs/source/api/models/submodels/porosity/reaction_driven_porosity_ode.rst +++ b/docs/source/api/models/submodels/porosity/reaction_driven_porosity_ode.rst @@ -3,6 +3,3 @@ Reaction-driven Model as an ODE .. autoclass:: pybamm.porosity.ReactionDrivenODE :members: - - - diff --git a/docs/source/api/models/submodels/thermal/base_thermal.rst b/docs/source/api/models/submodels/thermal/base_thermal.rst index fd3acc0edf..eb38b4934a 100644 --- a/docs/source/api/models/submodels/thermal/base_thermal.rst +++ b/docs/source/api/models/submodels/thermal/base_thermal.rst @@ -3,4 +3,3 @@ Base Thermal .. autoclass:: pybamm.thermal.BaseThermal :members: - diff --git a/docs/source/api/models/submodels/transport_efficiency/base_transport_efficiency.rst b/docs/source/api/models/submodels/transport_efficiency/base_transport_efficiency.rst index e24f0cba15..fc581a666a 100644 --- a/docs/source/api/models/submodels/transport_efficiency/base_transport_efficiency.rst +++ b/docs/source/api/models/submodels/transport_efficiency/base_transport_efficiency.rst @@ -3,4 +3,3 @@ Base Model .. autoclass:: pybamm.transport_efficiency.BaseModel :members: - diff --git a/docs/source/api/models/submodels/transport_efficiency/bruggeman_transport_efficiency.rst b/docs/source/api/models/submodels/transport_efficiency/bruggeman_transport_efficiency.rst index f50e825b09..f5e5f1c1bc 100644 --- a/docs/source/api/models/submodels/transport_efficiency/bruggeman_transport_efficiency.rst +++ b/docs/source/api/models/submodels/transport_efficiency/bruggeman_transport_efficiency.rst @@ -1,8 +1,5 @@ -Bruggeman Model +Bruggeman Model =============== .. autoclass:: pybamm.transport_efficiency.Bruggeman :members: - - - diff --git a/docs/source/api/models/submodels/transport_efficiency/index.rst b/docs/source/api/models/submodels/transport_efficiency/index.rst index fe7b640f68..fcdec7077f 100644 --- a/docs/source/api/models/submodels/transport_efficiency/index.rst +++ b/docs/source/api/models/submodels/transport_efficiency/index.rst @@ -6,4 +6,3 @@ transport_efficiency base_transport_efficiency bruggeman_transport_efficiency - diff --git a/docs/source/api/plotting/plot_summary_variables.rst b/docs/source/api/plotting/plot_summary_variables.rst index 35baeda605..746c501c5c 100644 --- a/docs/source/api/plotting/plot_summary_variables.rst +++ b/docs/source/api/plotting/plot_summary_variables.rst @@ -1,4 +1,4 @@ Plot Summary Variables ====================== -.. autofunction:: pybamm.plot_summary_variables \ No newline at end of file +.. autofunction:: pybamm.plot_summary_variables diff --git a/docs/source/api/plotting/plot_voltage_components.rst b/docs/source/api/plotting/plot_voltage_components.rst index 04d95e62cc..6954374d0c 100644 --- a/docs/source/api/plotting/plot_voltage_components.rst +++ b/docs/source/api/plotting/plot_voltage_components.rst @@ -3,4 +3,4 @@ Plot Voltage Components ======================= -.. autofunction:: pybamm.plot_voltage_components \ No newline at end of file +.. autofunction:: pybamm.plot_voltage_components diff --git a/docs/source/api/plotting/quick_plot.rst b/docs/source/api/plotting/quick_plot.rst index ef81719056..ff7576a00d 100644 --- a/docs/source/api/plotting/quick_plot.rst +++ b/docs/source/api/plotting/quick_plot.rst @@ -6,4 +6,4 @@ Quick Plot .. autoclass:: pybamm.QuickPlot :members: -.. autofunction:: pybamm.dynamic_plot \ No newline at end of file +.. autofunction:: pybamm.dynamic_plot diff --git a/docs/source/api/simulation.rst b/docs/source/api/simulation.rst index a50a67eb21..203420ad73 100644 --- a/docs/source/api/simulation.rst +++ b/docs/source/api/simulation.rst @@ -2,4 +2,4 @@ Simulation ========== .. autoclass:: pybamm.Simulation - :members: \ No newline at end of file + :members: diff --git a/docs/source/api/solvers/index.rst b/docs/source/api/solvers/index.rst index d87f003309..af2a8893dd 100644 --- a/docs/source/api/solvers/index.rst +++ b/docs/source/api/solvers/index.rst @@ -13,4 +13,3 @@ Solvers algebraic_solvers solution processed_variable - diff --git a/docs/source/api/spatial_methods/finite_volume.rst b/docs/source/api/spatial_methods/finite_volume.rst index f57c5e9e76..3b6122acc8 100644 --- a/docs/source/api/spatial_methods/finite_volume.rst +++ b/docs/source/api/spatial_methods/finite_volume.rst @@ -3,4 +3,3 @@ Finite Volume .. autoclass:: pybamm.FiniteVolume :members: - diff --git a/docs/source/user_guide/installation/GNU-linux.rst b/docs/source/user_guide/installation/GNU-linux.rst index 8f1ee50dbc..3bdeda9ad9 100644 --- a/docs/source/user_guide/installation/GNU-linux.rst +++ b/docs/source/user_guide/installation/GNU-linux.rst @@ -185,7 +185,7 @@ Then, to install PyBaMM as a `developer `__ 2.9.0 plot For generating simulation GIFs. `matplotlib `__ 2.0.0 plot To plot various battery models, and analyzing battery performance. -=========================================================== ================== ================== ================================================================== +=========================================================== ================== ================== ================================================================== .. _install.pandas_dependencies: @@ -127,7 +127,7 @@ Dependency `sphinx-autobuild `__ \- docs For re-building docs once triggered. ================================================================================================= ================== ================== ======================================================================= -.. _install.examples_dependencies: +.. _install.examples_dependencies: Examples dependencies ^^^^^^^^^^^^^^^^^^^^^ @@ -238,7 +238,7 @@ Dependency Before running ``pip install "pybamm[odes]"``, make sure to install ``scikits.odes`` build-time requirements as described `here `_ . Full installation guide ------------------------ +----------------------- Installing a specific version? Installing from source? Check the advanced installation pages below @@ -248,4 +248,4 @@ Installing a specific version? Installing from source? Check the advanced instal GNU-linux windows windows-wsl - install-from-source \ No newline at end of file + install-from-source diff --git a/docs/source/user_guide/installation/install-from-source.rst b/docs/source/user_guide/installation/install-from-source.rst index 82a7976852..0e3573cee2 100644 --- a/docs/source/user_guide/installation/install-from-source.rst +++ b/docs/source/user_guide/installation/install-from-source.rst @@ -90,7 +90,7 @@ If you'd rather do things yourself, 2. Compile and install SuiteSparse (PyBaMM only requires the ``KLU`` component). 3. Compile and install SUNDIALS. 4. Clone the pybind11 repository in the ``PyBaMM/`` directory (make sure the directory is named ``pybind11``). - + PyBaMM ships with a Python script that automates points 2. and 3. You can run it with @@ -193,7 +193,7 @@ Finally, to run the unit and the integration suites sequentially, use nox -s tests -Using the test runner +Using the test runner ~~~~~~~~~~~~~~~~~~~~~~ You can run unit tests for PyBaMM using diff --git a/pybamm/input/discharge_data/Enertech_cells/0.1C_discharge_displacement.txt b/pybamm/input/discharge_data/Enertech_cells/0.1C_discharge_displacement.txt index 1abab6f79c..ec8998b3c4 100644 --- a/pybamm/input/discharge_data/Enertech_cells/0.1C_discharge_displacement.txt +++ b/pybamm/input/discharge_data/Enertech_cells/0.1C_discharge_displacement.txt @@ -3742,4 +3742,4 @@ 36860 4.49083105587186E-7 36870 3.6003394272133456E-7 36880 2.7098410120201244E-7 -36881.8408095558 2.5459165129906363E-7 \ No newline at end of file +36881.8408095558 2.5459165129906363E-7 diff --git a/pybamm/input/discharge_data/Enertech_cells/0.5C_discharge_displacement.txt b/pybamm/input/discharge_data/Enertech_cells/0.5C_discharge_displacement.txt index 8ee457ce77..42103e4d32 100644 --- a/pybamm/input/discharge_data/Enertech_cells/0.5C_discharge_displacement.txt +++ b/pybamm/input/discharge_data/Enertech_cells/0.5C_discharge_displacement.txt @@ -785,4 +785,4 @@ 7290 5.629040101801396E-6 7300 5.185645939982822E-6 7310 4.742039959903541E-6 -7311.673930367749 4.667763172375133E-6 \ No newline at end of file +7311.673930367749 4.667763172375133E-6 diff --git a/pybamm/input/discharge_data/Enertech_cells/1C_discharge_displacement.txt b/pybamm/input/discharge_data/Enertech_cells/1C_discharge_displacement.txt index 69f31d5e6c..c8881d82e0 100644 --- a/pybamm/input/discharge_data/Enertech_cells/1C_discharge_displacement.txt +++ b/pybamm/input/discharge_data/Enertech_cells/1C_discharge_displacement.txt @@ -414,4 +414,4 @@ 3580 1.3950084177824084E-5 3590 1.3086398528538203E-5 3600 1.2219619567992016E-5 -3609.1611221134444 1.1422884433792557E-5 \ No newline at end of file +3609.1611221134444 1.1422884433792557E-5 diff --git a/pybamm/input/discharge_data/Enertech_cells/stn_2C.txt b/pybamm/input/discharge_data/Enertech_cells/stn_2C.txt index 2b924bdb92..1517501646 100755 --- a/pybamm/input/discharge_data/Enertech_cells/stn_2C.txt +++ b/pybamm/input/discharge_data/Enertech_cells/stn_2C.txt @@ -1,5 +1,5 @@ -# Negative particle surface tangetial stress close to the separator -# for the Enertech cells Ai2020 JES +# Negative particle surface tangetial stress close to the separator +# for the Enertech cells Ai2020 JES # time [s] and normalised stress sigma_t_surf_n/E_n 0,-1.0741e-17 2,0.00031276 diff --git a/pybamm/input/discharge_data/Enertech_cells/stp_2C.txt b/pybamm/input/discharge_data/Enertech_cells/stp_2C.txt index 0cf5eb9b13..2190ad2fbf 100755 --- a/pybamm/input/discharge_data/Enertech_cells/stp_2C.txt +++ b/pybamm/input/discharge_data/Enertech_cells/stp_2C.txt @@ -1,4 +1,4 @@ -# Positive particle surface tangetial stress close to the separator +# Positive particle surface tangetial stress close to the separator # for the Enertech cells Ai2020 JES # time [s] and normalised stress sigma_t_surf_p/E_p 0,2.207e-18 diff --git a/pybamm/input/parameters/lithium_ion/data/graphite_LGM50_ocp_Chen2020.csv b/pybamm/input/parameters/lithium_ion/data/graphite_LGM50_ocp_Chen2020.csv index c43da295d5..15615f5bb2 100644 --- a/pybamm/input/parameters/lithium_ion/data/graphite_LGM50_ocp_Chen2020.csv +++ b/pybamm/input/parameters/lithium_ion/data/graphite_LGM50_ocp_Chen2020.csv @@ -250,4 +250,4 @@ 0.9704444444444444,0.07871961454862104 0.9802222222222222,0.07782495680237907 0.99,0.07693029905613709 -1,0.0760153081792987 \ No newline at end of file +1,0.0760153081792987 diff --git a/pybamm/input/parameters/lithium_ion/data/graphite_ocp_Enertech_Ai2020.csv b/pybamm/input/parameters/lithium_ion/data/graphite_ocp_Enertech_Ai2020.csv index 8a5bce2874..abde62a61c 100644 --- a/pybamm/input/parameters/lithium_ion/data/graphite_ocp_Enertech_Ai2020.csv +++ b/pybamm/input/parameters/lithium_ion/data/graphite_ocp_Enertech_Ai2020.csv @@ -126,4 +126,4 @@ 0.999241066,0.030242658 0.999746961,0.024850768 0.999936448,0.019251502 -1,0.004994678 \ No newline at end of file +1,0.004994678 diff --git a/pybamm/input/parameters/lithium_ion/data/lico2_ocp_Ai2020.csv b/pybamm/input/parameters/lithium_ion/data/lico2_ocp_Ai2020.csv index 2c81422639..b1053f1a39 100644 --- a/pybamm/input/parameters/lithium_ion/data/lico2_ocp_Ai2020.csv +++ b/pybamm/input/parameters/lithium_ion/data/lico2_ocp_Ai2020.csv @@ -1,4 +1,4 @@ -# OCP for lico2 from Rieger 2016 +# OCP for lico2 from Rieger 2016 # stoichiometry , OCP [V] 0.4,4.390781177520233 0.401,4.387755138269558 diff --git a/pybamm/input/parameters/lithium_ion/data/nca_ocp_Kim2011_data.csv b/pybamm/input/parameters/lithium_ion/data/nca_ocp_Kim2011_data.csv index dd00060753..8057f34f56 100644 --- a/pybamm/input/parameters/lithium_ion/data/nca_ocp_Kim2011_data.csv +++ b/pybamm/input/parameters/lithium_ion/data/nca_ocp_Kim2011_data.csv @@ -72,4 +72,4 @@ 0.9896421223593032, 3.204894695680104 0.9905703960976598, 3.1496257442302342 0.9915055751666949, 3.104277451188519 -0.9933828386354436, 3.023501523513243 \ No newline at end of file +0.9933828386354436, 3.023501523513243 diff --git a/pybamm/input/parameters/lithium_ion/data/nmc_LGM50_ocp_Chen2020.csv b/pybamm/input/parameters/lithium_ion/data/nmc_LGM50_ocp_Chen2020.csv index 7dc9adc71c..8a2edc1ab0 100644 --- a/pybamm/input/parameters/lithium_ion/data/nmc_LGM50_ocp_Chen2020.csv +++ b/pybamm/input/parameters/lithium_ion/data/nmc_LGM50_ocp_Chen2020.csv @@ -240,4 +240,4 @@ 0.903203643476430,3.56849220000000 0.905926128940627,3.56721330000000 # extra points to avoid extrapolation -1,3.52302166875714 \ No newline at end of file +1,3.52302166875714 diff --git a/pybamm/models/full_battery_models/base_battery_model.py b/pybamm/models/full_battery_models/base_battery_model.py index 7a39874108..db0e38710a 100644 --- a/pybamm/models/full_battery_models/base_battery_model.py +++ b/pybamm/models/full_battery_models/base_battery_model.py @@ -44,9 +44,9 @@ class BatteryModelOptions(pybamm.FuzzyDict): Sets the current collector model to use. Can be "uniform" (default), "potential pair" or "potential pair quite conductive". * "diffusivity" : str - Sets the model for the diffusivity. Can be "single" - (default) or "current sigmoid". A 2-tuple can be provided for different - behaviour in negative and positive electrodes. + Sets the model for the diffusivity. Can be "single" + (default) or "current sigmoid". A 2-tuple can be provided for different + behaviour in negative and positive electrodes. * "dimensionality" : int Sets the dimension of the current collector problem. Can be 0 (default), 1 or 2. @@ -54,9 +54,9 @@ class BatteryModelOptions(pybamm.FuzzyDict): Can be "default" (default), "full", "leading order", "composite" or "integrated". * "exchange-current density" : str - Sets the model for the exchange-current density. Can be "single" - (default) or "current sigmoid". A 2-tuple can be provided for different - behaviour in negative and positive electrodes. + Sets the model for the exchange-current density. Can be "single" + (default) or "current sigmoid". A 2-tuple can be provided for different + behaviour in negative and positive electrodes. * "hydrolysis" : str Whether to include hydrolysis in the model. Only implemented for lead-acid models. Can be "false" (default) or "true". If "true", then @@ -81,9 +81,9 @@ class BatteryModelOptions(pybamm.FuzzyDict): A 2-tuple can be provided for different behaviour in negative and positive electrodes. * "open-circuit potential" : str - Sets the model for the open circuit potential. Can be "single" - (default) or "current sigmoid". A 2-tuple can be provided for different - behaviour in negative and positive electrodes. + Sets the model for the open circuit potential. Can be "single" + (default) or "current sigmoid". A 2-tuple can be provided for different + behaviour in negative and positive electrodes. * "operating mode" : str Sets the operating mode for the model. This determines how the current is set. Can be: @@ -103,7 +103,7 @@ class BatteryModelOptions(pybamm.FuzzyDict): * "particle" : str Sets the submodel to use to describe behaviour within the particle. Can be "Fickian diffusion" (default), "uniform profile", - "quadratic profile", or "quartic profile". A 2-tuple can be provided + "quadratic profile", or "quartic profile". A 2-tuple can be provided for different behaviour in negative and positive electrodes. * "particle mechanics" : str Sets the model to account for mechanical effects such as particle diff --git a/pybamm/models/submodels/interface/kinetics/inverse_kinetics/__init__.py b/pybamm/models/submodels/interface/kinetics/inverse_kinetics/__init__.py index 8b13789179..e69de29bb2 100644 --- a/pybamm/models/submodels/interface/kinetics/inverse_kinetics/__init__.py +++ b/pybamm/models/submodels/interface/kinetics/inverse_kinetics/__init__.py @@ -1 +0,0 @@ - diff --git a/pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp b/pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp index e56b0902b2..310575742d 100644 --- a/pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp +++ b/pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp @@ -41,7 +41,7 @@ CasadiFunctions::CasadiFunctions( const Function &mass_action, const Function &sens, const Function &events, const int n_s, int n_e, const int n_p, const Options& options) : number_of_states(n_s), number_of_events(n_e), number_of_parameters(n_p), - number_of_nnz(jac_times_cjmass_nnz), + number_of_nnz(jac_times_cjmass_nnz), jac_bandwidth_lower(jac_bandwidth_lower), jac_bandwidth_upper(jac_bandwidth_upper), rhs_alg(rhs_alg), jac_times_cjmass(jac_times_cjmass), jac_action(jac_action), @@ -67,7 +67,7 @@ CasadiFunctions::CasadiFunctions( } inputs.resize(inputs_length); - + } realtype *CasadiFunctions::get_tmp_state_vector() { return tmp_state_vector.data(); } diff --git a/pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp b/pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp index 23a24d5372..67bb2793ae 100644 --- a/pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp +++ b/pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp @@ -10,8 +10,8 @@ create_casadi_solver(int number_of_states, int number_of_parameters, const Function &rhs_alg, const Function &jac_times_cjmass, const np_array_int &jac_times_cjmass_colptrs, const np_array_int &jac_times_cjmass_rowvals, - const int jac_times_cjmass_nnz, - const int jac_bandwidth_lower, const int jac_bandwidth_upper, + const int jac_times_cjmass_nnz, + const int jac_bandwidth_lower, const int jac_bandwidth_upper, const Function &jac_action, const Function &mass_action, const Function &sens, const Function &events, const int number_of_events, @@ -26,7 +26,7 @@ create_casadi_solver(int number_of_states, int number_of_parameters, options_cpp); return new CasadiSolver(atol_np, rel_tol, rhs_alg_id, number_of_parameters, - number_of_events, jac_times_cjmass_nnz, + number_of_events, jac_times_cjmass_nnz, jac_bandwidth_lower, jac_bandwidth_upper, std::move(functions), options_cpp); } @@ -169,7 +169,7 @@ CasadiSolver::CasadiSolver(np_array atol_np, double rel_tol, } else if (options.linear_solver == "SUNLinSol_Band") { - DEBUG("\tsetting SUNLinSol_Band linear solver"); + DEBUG("\tsetting SUNLinSol_Band linear solver"); #if SUNDIALS_VERSION_MAJOR >= 6 LS = SUNLinSol_Band(yy, J, sunctx); #else @@ -302,15 +302,15 @@ Solution CasadiSolver::solve(np_array t_np, np_array y0_np, np_array yp0_np, if (y0.size() != number_of_states + number_of_parameters * number_of_states) { throw std::domain_error( - "y0 has wrong size. Expected " + - std::to_string(number_of_states + number_of_parameters * number_of_states) + + "y0 has wrong size. Expected " + + std::to_string(number_of_states + number_of_parameters * number_of_states) + " but got " + std::to_string(y0.size())); } if (yp0.size() != number_of_states + number_of_parameters * number_of_states) { throw std::domain_error( - "yp0 has wrong size. Expected " + - std::to_string(number_of_states + number_of_parameters * number_of_states) + + "yp0 has wrong size. Expected " + + std::to_string(number_of_states + number_of_parameters * number_of_states) + " but got " + std::to_string(yp0.size())); } diff --git a/pybamm/solvers/c_solvers/idaklu/casadi_solver.hpp b/pybamm/solvers/c_solvers/idaklu/casadi_solver.hpp index 09c4434d5b..75bc73e9d3 100644 --- a/pybamm/solvers/c_solvers/idaklu/casadi_solver.hpp +++ b/pybamm/solvers/c_solvers/idaklu/casadi_solver.hpp @@ -48,8 +48,8 @@ create_casadi_solver(int number_of_states, int number_of_parameters, const Function &rhs_alg, const Function &jac_times_cjmass, const np_array_int &jac_times_cjmass_colptrs, const np_array_int &jac_times_cjmass_rowvals, - const int jac_times_cjmass_nnz, - const int jac_bandwidth_lower, const int jac_bandwidth_upper, + const int jac_times_cjmass_nnz, + const int jac_bandwidth_lower, const int jac_bandwidth_upper, const Function &jac_action, const Function &mass_action, const Function &sens, const Function &event, const int number_of_events, diff --git a/pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.cpp b/pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.cpp index eaf383cda4..8a3d96966f 100644 --- a/pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.cpp +++ b/pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.cpp @@ -172,7 +172,7 @@ int jacobian_casadi(realtype tt, realtype cj, N_Vector yy, N_Vector yp, p_python_functions->jac_times_cjmass(); - if (p_python_functions->options.using_banded_matrix) + if (p_python_functions->options.using_banded_matrix) { // copy data from temporary matrix to the banded matrix auto jac_colptrs = p_python_functions->jac_times_cjmass_colptrs.data(); @@ -187,7 +187,7 @@ int jacobian_casadi(realtype tt, realtype cj, N_Vector yy, N_Vector yp, SM_COLUMN_ELEMENT_B(banded_col, row_ij, col_ij) = value_ij; } } - } + } else if (p_python_functions->options.using_sparse_matrix) { @@ -279,7 +279,7 @@ int sensitivities_casadi(int Ns, realtype t, N_Vector yy, N_Vector yp, } // resvalsS now has (∂F/∂p i ) p_python_functions->sens(); - + for (int i = 0; i < np; i++) { // put (∂F/∂y)s i (t) in tmp diff --git a/pybamm/solvers/c_solvers/idaklu/common.hpp b/pybamm/solvers/c_solvers/idaklu/common.hpp index 1931f8cb61..d6ddb5c16b 100644 --- a/pybamm/solvers/c_solvers/idaklu/common.hpp +++ b/pybamm/solvers/c_solvers/idaklu/common.hpp @@ -12,7 +12,7 @@ #if SUNDIALS_VERSION_MAJOR >= 6 - #include + #include #endif #include /* access to KLU linear solver */ @@ -37,7 +37,7 @@ using np_array_dense = py::array_t; #ifdef NDEBUG -#define DEBUG(x) +#define DEBUG(x) #else #define DEBUG(x) do { std::cerr << __FILE__ << ':' << __LINE__ << ' ' << x << std::endl; } while (0) #endif diff --git a/pybamm/solvers/c_solvers/idaklu/options.cpp b/pybamm/solvers/c_solvers/idaklu/options.cpp index 2a5ed58d9c..33998470ed 100644 --- a/pybamm/solvers/c_solvers/idaklu/options.cpp +++ b/pybamm/solvers/c_solvers/idaklu/options.cpp @@ -2,7 +2,7 @@ #include #include - + using namespace std::string_literals; Options::Options(py::dict options) @@ -35,7 +35,7 @@ Options::Options(py::dict options) else { throw std::domain_error( - "Unknown jacobian type \""s + jacobian + + "Unknown jacobian type \""s + jacobian + "\". Should be one of \"sparse\", \"banded\", \"dense\", \"matrix-free\" or \"none\"."s ); } @@ -97,7 +97,7 @@ Options::Options(py::dict options) { throw std::domain_error( "Unknown linear solver or incompatible options. " - "jacobian = \"" + jacobian + "\" linear solver = \"" + linear_solver + "\"" + "jacobian = \"" + jacobian + "\" linear solver = \"" + linear_solver + "\"" ); } @@ -106,7 +106,7 @@ Options::Options(py::dict options) if (preconditioner != "none" && preconditioner != "BBDP") { throw std::domain_error( - "Unknown preconditioner \""s + preconditioner + + "Unknown preconditioner \""s + preconditioner + "\", use one of \"BBDP\" or \"none\""s ); } diff --git a/pybamm/solvers/c_solvers/idaklu/options.hpp b/pybamm/solvers/c_solvers/idaklu/options.hpp index 30e6fc634d..db5f136a01 100644 --- a/pybamm/solvers/c_solvers/idaklu/options.hpp +++ b/pybamm/solvers/c_solvers/idaklu/options.hpp @@ -9,8 +9,8 @@ struct Options { bool using_banded_matrix; bool using_iterative_solver; std::string jacobian; - std::string linear_solver; // klu, lapack, spbcg - std::string preconditioner; // spbcg + std::string linear_solver; // klu, lapack, spbcg + std::string preconditioner; // spbcg int linsol_max_iterations; int precon_half_bandwidth; int precon_half_bandwidth_keep; diff --git a/pybamm/solvers/c_solvers/idaklu/python.cpp b/pybamm/solvers/c_solvers/idaklu/python.cpp index a1803988d4..9ec018109e 100644 --- a/pybamm/solvers/c_solvers/idaklu/python.cpp +++ b/pybamm/solvers/c_solvers/idaklu/python.cpp @@ -14,10 +14,10 @@ class PybammFunctions const jac_get_type &get_jac_data_in, const jac_get_type &get_jac_row_vals_in, const jac_get_type &get_jac_col_ptrs_in, - const event_type &event, + const event_type &event, const int n_s, int n_e, const int n_p, const np_array &inputs) - : number_of_states(n_s), number_of_events(n_e), + : number_of_states(n_s), number_of_events(n_e), number_of_parameters(n_p), py_res(res), py_jac(jac), py_sens(sens), @@ -48,11 +48,11 @@ class PybammFunctions void sensitivities( std::vector& resvalS, - const double t, const np_array& y, const np_array& yp, - const std::vector& yS, const std::vector& ypS) + const double t, const np_array& y, const np_array& yp, + const std::vector& yS, const std::vector& ypS) { // this function evaluates the sensitivity equations required by IDAS, - // returning them in resvalS, which is preallocated as a numpy array + // returning them in resvalS, which is preallocated as a numpy array // of size (np, n), where n is the number of states and np is the number // of parameters // @@ -199,11 +199,11 @@ int events(realtype t, N_Vector yy, N_Vector yp, realtype *events_ptr, return (0); } -int sensitivities(int Ns, realtype t, N_Vector yy, N_Vector yp, - N_Vector resval, N_Vector *yS, N_Vector *ypS, N_Vector *resvalS, +int sensitivities(int Ns, realtype t, N_Vector yy, N_Vector yp, + N_Vector resval, N_Vector *yS, N_Vector *ypS, N_Vector *resvalS, void *user_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) { -// This function computes the sensitivity residual for all sensitivity -// equations. It must compute the vectors +// This function computes the sensitivity residual for all sensitivity +// equations. It must compute the vectors // (∂F/∂y)s i (t)+(∂F/∂ ẏ) ṡ i (t)+(∂F/∂p i ) and store them in resvalS[i]. // Ns is the number of sensitivities. // t is the current value of the independent variable. @@ -212,15 +212,15 @@ int sensitivities(int Ns, realtype t, N_Vector yy, N_Vector yp, // resval contains the current value F of the original DAE residual. // yS contains the current values of the sensitivities s i . // ypS contains the current values of the sensitivity derivatives ṡ i . -// resvalS contains the output sensitivity residual vectors. +// resvalS contains the output sensitivity residual vectors. // Memory allocation for resvalS is handled within idas. // user data is a pointer to user data. -// tmp1, tmp2, tmp3 are N Vectors of length N which can be used as +// tmp1, tmp2, tmp3 are N Vectors of length N which can be used as // temporary storage. // -// Return value An IDASensResFn should return 0 if successful, +// Return value An IDASensResFn should return 0 if successful, // a positive value if a recoverable error -// occurred (in which case idas will attempt to correct), +// occurred (in which case idas will attempt to correct), // or a negative value if it failed unrecoverably (in which case the integration is halted and IDA SRES FAIL is returned) // PybammFunctions *python_functions_ptr = @@ -232,7 +232,7 @@ int sensitivities(int Ns, realtype t, N_Vector yy, N_Vector yp, // memory managed by sundials, so pass a destructor that does nothing auto state_vector_shape = std::vector{n, 1}; - np_array y_np = np_array(state_vector_shape, N_VGetArrayPointer(yy), + np_array y_np = np_array(state_vector_shape, N_VGetArrayPointer(yy), py::capsule(&yy, [](void* p) {})); np_array yp_np = np_array(state_vector_shape, N_VGetArrayPointer(yp), py::capsule(&yp, [](void* p) {})); @@ -252,7 +252,7 @@ int sensitivities(int Ns, realtype t, N_Vector yy, N_Vector yp, std::vector resvalS_np(np); for (int i = 0; i < np; i++) { auto capsule = py::capsule(resvalS + i, [](void* p) {}); - resvalS_np[i] = np_array(state_vector_shape, + resvalS_np[i] = np_array(state_vector_shape, N_VGetArrayPointer(resvalS[i]), capsule); } @@ -266,12 +266,12 @@ int sensitivities(int Ns, realtype t, N_Vector yy, N_Vector yp, /* main program */ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np, - residual_type res, jacobian_type jac, + residual_type res, jacobian_type jac, sensitivities_type sens, - jac_get_type gjd, jac_get_type gjrv, jac_get_type gjcp, + jac_get_type gjd, jac_get_type gjrv, jac_get_type gjcp, int nnz, event_type event, int number_of_events, int use_jacobian, np_array rhs_alg_id, - np_array atol_np, double rel_tol, np_array inputs, + np_array atol_np, double rel_tol, np_array inputs, int number_of_parameters) { auto t = t_np.unchecked<1>(); @@ -374,7 +374,7 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np, if (number_of_parameters > 0) { - IDASensInit(ida_mem, number_of_parameters, + IDASensInit(ida_mem, number_of_parameters, IDA_SIMULTANEOUS, sensitivities, yyS, ypS); IDASensEEtolerances(ida_mem); } @@ -433,7 +433,7 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np, y_return[t_i * number_of_states + j] = yval[j]; } for (int j = 0; j < number_of_parameters; j++) { - const int base_index = j * number_of_timesteps * number_of_states + const int base_index = j * number_of_timesteps * number_of_states + t_i * number_of_states; for (int k = 0; k < number_of_states; k++) { yS_return[base_index + k] = ySval[j][k]; @@ -468,11 +468,10 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np, np_array y_ret = np_array(t_i * number_of_states, &y_return[0]); np_array yS_ret = np_array( std::vector{number_of_parameters, number_of_timesteps, number_of_states}, - &yS_return[0] + &yS_return[0] ); Solution sol(retval, t_ret, y_ret, yS_ret); return sol; } - diff --git a/pybamm/solvers/c_solvers/idaklu/python.hpp b/pybamm/solvers/c_solvers/idaklu/python.hpp index 8c29bbc496..8ae73f2a90 100644 --- a/pybamm/solvers/c_solvers/idaklu/python.hpp +++ b/pybamm/solvers/c_solvers/idaklu/python.hpp @@ -9,9 +9,9 @@ using residual_type = std::function< np_array(realtype, np_array, np_array, np_array) >; using sensitivities_type = std::function&, realtype, const np_array&, + std::vector&, realtype, const np_array&, const np_array&, - const np_array&, const std::vector&, + const np_array&, const std::vector&, const std::vector& )>; using jacobian_type = std::function; @@ -24,9 +24,9 @@ using jac_get_type = std::function; Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np, - residual_type res, jacobian_type jac, + residual_type res, jacobian_type jac, sensitivities_type sens, - jac_get_type gjd, jac_get_type gjrv, jac_get_type gjcp, + jac_get_type gjd, jac_get_type gjrv, jac_get_type gjcp, int nnz, event_type event, int number_of_events, int use_jacobian, np_array rhs_alg_id, np_array atol_np, double rel_tol, np_array inputs, diff --git a/run-tests.py b/run-tests.py index 4705fd37a5..5d4bb65b65 100755 --- a/run-tests.py +++ b/run-tests.py @@ -187,7 +187,7 @@ def test_notebook(path, executable="python"): print("Test " + path + " ... ", end="") sys.stdout.flush() - # Make sure the notebook has a + # Make sure the notebook has a # "%pip install pybamm[plot,cite] -q" command, for using Google Colab with open(path, "r") as f: if "%pip install pybamm[plot,cite] -q" not in f.read(): diff --git a/scripts/replace-cmake/sundials-3.1.1/CMakeLists.txt b/scripts/replace-cmake/sundials-3.1.1/CMakeLists.txt index 342ddf4f9b..81f4267c22 100644 --- a/scripts/replace-cmake/sundials-3.1.1/CMakeLists.txt +++ b/scripts/replace-cmake/sundials-3.1.1/CMakeLists.txt @@ -36,7 +36,7 @@ SET(PACKAGE_NAME "SUNDIALS") SET(PACKAGE_STRING "SUNDIALS 3.1.1") SET(PACKAGE_TARNAME "sundials") -# set SUNDIALS version numbers +# set SUNDIALS version numbers # (use "" for the version label if none is needed) SET(PACKAGE_VERSION_MAJOR "3") SET(PACKAGE_VERSION_MINOR "1") @@ -387,7 +387,7 @@ OPTION(HYPRE_ENABLE "Enable hypre support" OFF) # Using hypre requres building with MPI enabled IF(HYPRE_ENABLE AND NOT MPI_ENABLE) - PRINT_WARNING("MPI not enabled - Disabling hypre" + PRINT_WARNING("MPI not enabled - Disabling hypre" "Set MPI_ENABLE to ON to use parhyp") FORCE_VARIABLE(HYPRE_ENABLE BOOL "Enable hypre support" OFF) ENDIF() @@ -399,7 +399,7 @@ OPTION(PETSC_ENABLE "Enable PETSc support" OFF) # Using PETSc requires building with MPI enabled IF(PETSC_ENABLE AND NOT MPI_ENABLE) - PRINT_WARNING("MPI not enabled - Disabling PETSc" + PRINT_WARNING("MPI not enabled - Disabling PETSc" "Set MPI_ENABLE to ON to use PETSc") FORCE_VARIABLE(PETSC_ENABLE BOOL "Enable PETSc support" OFF) ENDIF() @@ -456,7 +456,7 @@ ENDIF() SET(DOCSTR "Build ARKode F90 examples") IF(FCMIX_ENABLE AND BUILD_ARKODE) SHOW_VARIABLE(EXAMPLES_ENABLE_F90 BOOL "${DOCSTR}" OFF) - # Fortran90 examples do not support single or extended precision + # Fortran90 examples do not support single or extended precision # NOTE: This check can be removed after Fortran configure file is integrated into examples IF(SUNDIALS_PRECISION MATCHES "EXTENDED" OR SUNDIALS_PRECISION MATCHES "SINGLE") PRINT_WARNING("F90 examples are not compatible with ${SUNDIALS_PRECISION} precision" @@ -540,7 +540,7 @@ IF(EXAMPLES_ENABLED) SET(EXAMPLES_INSTALL_PATH "${CMAKE_INSTALL_PREFIX}/examples" CACHE STRING "Output directory for installing example files" FORCE) ENDIF(NOT EXAMPLES_INSTALL_PATH) - + # create test_install target and directory for running smoke tests after # installation ADD_CUSTOM_TARGET(test_install) @@ -565,7 +565,7 @@ ELSE(EXAMPLES_ENABLED) HIDE_VARIABLE(EXAMPLES_INSTALL) HIDE_VARIABLE(EXAMPLES_INSTALL_PATH) - + ENDIF(EXAMPLES_ENABLED) # --------------------------------------------------------------- @@ -796,7 +796,7 @@ IF(PTHREAD_ENABLE) IF(CMAKE_USE_PTHREADS_INIT) message(STATUS "Using Pthreads") SET(PTHREADS_FOUND TRUE) - # SGS + # SGS ELSE() message(STATUS "Disabling Pthreads support, could not determine compiler flags") endif() @@ -814,7 +814,7 @@ ENDIF() if(CUDA_ENABLE) find_package(CUDA) - + if (CUDA_FOUND) #message("CUDA found!") set(CUDA_NVCC_FLAGS "-lineinfo") @@ -1026,7 +1026,7 @@ IF(HYPRE_ENABLE) PRINT_WARNING("HYPRE not functional - support will not be provided" "Found hypre library, test code does not work") ENDIF(HYPRE_LIBRARIES AND NOT HYPRE_FOUND) - + ELSE() HIDE_VARIABLE(HYPRE_INCLUDE_DIR) @@ -1070,7 +1070,7 @@ ENDIF() # =============================================================== -# Add source and configuration files +# Add source and configuration files # =============================================================== # --------------------------------------------------------------- @@ -1141,11 +1141,11 @@ IF(PETSC_FOUND) ENDIF(PETSC_FOUND) IF(CUDA_FOUND) - ADD_SUBDIRECTORY(src/nvec_cuda) + ADD_SUBDIRECTORY(src/nvec_cuda) ENDIF(CUDA_FOUND) IF(RAJA_FOUND) - ADD_SUBDIRECTORY(src/nvec_raja) + ADD_SUBDIRECTORY(src/nvec_raja) ENDIF(RAJA_FOUND) # ARKODE library @@ -1241,7 +1241,7 @@ IF(EXAMPLES_ENABLED) SET(CFLAGS "${CMAKE_C_FLAGS_RELEASE}") SET(LDFLAGS "${CMAKE_EXE_LINKER_FLAGS_RELEASE}") LIST2STRING(EXTRA_LINK_LIBS LIBS) - + IF(CXX_FOUND) SET(CXX "${CMAKE_CXX_COMPILER}") SET(CXX_LNKR "${CMAKE_CXX_COMPILER}") @@ -1378,7 +1378,7 @@ IF(EXAMPLES_ENABLED) IF(MPIF90_FOUND) ADD_SUBDIRECTORY(examples/arkode/F90_parallel) ENDIF() - ENDIF() + ENDIF() ENDIF(BUILD_ARKODE) # add CVODE examples @@ -1411,7 +1411,7 @@ IF(EXAMPLES_ENABLED) ADD_SUBDIRECTORY(examples/cvode/cuda) ENDIF() ENDIF(EXAMPLES_ENABLE_CUDA) - # raja examples + # raja examples IF(EXAMPLES_ENABLE_RAJA) IF(RAJA_ENABLE AND RAJA_FOUND) ADD_SUBDIRECTORY(examples/cvode/raja) @@ -1568,11 +1568,11 @@ IF(EXAMPLES_ENABLED) IF(CUDA_FOUND) ADD_SUBDIRECTORY(examples/nvector/cuda) ENDIF(CUDA_FOUND) - + IF(RAJA_FOUND) ADD_SUBDIRECTORY(examples/nvector/raja) ENDIF(RAJA_FOUND) - + ENDIF(EXAMPLES_ENABLED) # --------------------------------------------------------------- diff --git a/scripts/replace-cmake/sundials-4.1.0/CMakeLists.txt b/scripts/replace-cmake/sundials-4.1.0/CMakeLists.txt index fdd1bc206e..fc8acbddc9 100644 --- a/scripts/replace-cmake/sundials-4.1.0/CMakeLists.txt +++ b/scripts/replace-cmake/sundials-4.1.0/CMakeLists.txt @@ -1149,4 +1149,3 @@ INSTALL( FILES ${PROJECT_SOURCE_DIR}/NOTICE DESTINATION include/sundials ) - diff --git a/scripts/replace-cmake/sundials-5.0.0/CMakeLists.txt b/scripts/replace-cmake/sundials-5.0.0/CMakeLists.txt index fdd1bc206e..fc8acbddc9 100644 --- a/scripts/replace-cmake/sundials-5.0.0/CMakeLists.txt +++ b/scripts/replace-cmake/sundials-5.0.0/CMakeLists.txt @@ -1149,4 +1149,3 @@ INSTALL( FILES ${PROJECT_SOURCE_DIR}/NOTICE DESTINATION include/sundials ) -