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Merge branch 'master' into pbrubeck/zany-point-evaluation
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‎.github/workflows/build.yml‎

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@@ -39,7 +39,8 @@ jobs:
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FIREDRAKE_CI: 1
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PYOP2_CI_TESTS: 1
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PYOP2_SPMD_STRICT: 1
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EXTRA_PYTEST_ARGS: --splitting-algorithm least_duration --timeout=600 --timeout-method=thread -o faulthandler_timeout=660 firedrake-repo/tests/firedrake
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EXTRA_PYTEST_ARGS: --splitting-algorithm least_duration --timeout=600 --timeout-method=thread -o faulthandler_timeout=660
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PYTEST_MPI_MAX_NPROCS: 8
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steps:
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- name: Fix HOME
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# For unknown reasons GitHub actions overwrite HOME to /github/home
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cd petsc
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python3 ../firedrake-repo/scripts/firedrake-configure \
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--arch ${{ matrix.arch }} --show-petsc-configure-options | \
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xargs -L1 ./configure --with-make-np=12 --download-slepc
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xargs -L1 ./configure --with-make-np=8 --download-slepc
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make PETSC_DIR=/__w/firedrake/firedrake/petsc PETSC_ARCH=arch-firedrake-${{ matrix.arch }}
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make check
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echo "PETSC_DIR=/__w/firedrake/firedrake/petsc" >> "$GITHUB_ENV"
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firedrake-check
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timeout-minutes: 5
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- name: Run tests (nprocs = 1)
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- name: Run TSFC tests
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# Run even if earlier tests failed
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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: # Use pytest-xdist here so we can have a single collated output (not possible
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: # for parallel tests)
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firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/tsfc
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timeout-minutes: 60
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- name: Run PyOP2 tests
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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: # Use pytest-xdist here so we can have a single collated output (not possible
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: # for parallel tests)
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firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
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firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
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firedrake-run-split-tests 3 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
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firedrake-run-split-tests 4 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
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timeout-minutes: 15
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- name: Run Firedrake tests (nprocs = 1)
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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: # Use pytest-xdist here so we can have a single collated output (not possible
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: # for parallel tests)
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firedrake-run-split-tests 1 1 "-n 12 $EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 60
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- name: Run tests (nprocs = 2)
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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firedrake-run-split-tests 2 6 "$EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 30
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- name: Run tests (nprocs = 3)
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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firedrake-run-split-tests 3 4 "$EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 3 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 60
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- name: Run tests (nprocs = 4)
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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firedrake-run-split-tests 4 3 "$EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 4 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 15
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- name: Run tests (nprocs = 5)
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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firedrake-run-split-tests 5 2 "$EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 5 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 15
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- name: Run tests (nprocs = 6)
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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firedrake-run-split-tests 6 2 "$EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 6 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 15
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- name: Run tests (nprocs = 7)
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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firedrake-run-split-tests 7 1 "$EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 7 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 15
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- name: Run tests (nprocs = 8)
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if: ${{ success() || steps.install.conclusion == 'success' }}
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if: success() || steps.install.conclusion == 'success'
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run: |
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. venv/bin/activate
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firedrake-run-split-tests 8 1 "$EXTRA_PYTEST_ARGS"
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firedrake-run-split-tests 8 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
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timeout-minutes: 15
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- name: Run Gusto smoke tests
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. venv/bin/activate
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git clone --depth 1 https://github.com/firedrakeproject/gusto.git gusto-repo
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pip install --verbose ./gusto-repo
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python -m pytest -n 12 --verbose \
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python -m pytest -n 8 --verbose \
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gusto-repo/integration-tests/balance/test_saturated_balance.py \
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gusto-repo/integration-tests/equations/test_thermal_sw.py \
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gusto-repo/integration-tests/transport/test_embedded_dg_advection.py
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timeout-minutes: 10
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- name: Run Thetis smoke tests
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if: (success() || steps.install.conclusion == 'success') && matrix.arch == 'default'
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run: |
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. venv/bin/activate
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git clone --depth 1 https://github.com/thetisproject/thetis.git thetis-repo
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pip install --verbose ./thetis-repo
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python -m pytest -n 8 --verbose thetis-repo/test_adjoint/test_swe_adjoint.py
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timeout-minutes: 10
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- name: Run spyro smoke tests
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if: (success() || steps.install.conclusion == 'success') && matrix.arch == 'default'
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run: |
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- name: Setup Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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python-version: "3.12"
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- name: Install deps
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run: pip install requests packaging
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- name: Zenodo API canary
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uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: "zenodo-canary"
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name: zenodo-canary
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path: firedrake-install.log

‎.github/workflows/pyop2.yml‎

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This file was deleted.

‎docker/Dockerfile.vanilla‎

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@@ -44,7 +44,7 @@ RUN git clone --depth 1 --branch $(python3 /opt/firedrake-configure --show-petsc
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&& cd /opt/petsc \
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&& python3 /opt/firedrake-configure --arch $ARCH --show-petsc-configure-options | \
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sed "s/$/ --COPTFLAGS='-O3 -mtune=generic' --CXXOPTFLAGS='-O3 -mtune=generic' --FOPTFLAGS='-O3 -mtune=generic'/" | \
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xargs -L1 ./configure --with-make-np=12 --download-slepc \
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xargs -L1 ./configure --with-make-np=8 --download-slepc \
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&& make \
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&& make check \
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&& rm -rf ./**/externalpackages \

‎docs/source/aims_25.rst‎

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:orphan: true
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.. title:: Finite Element Course at AIMS Rwanda
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Finite Element Course at AIMS Rwanda
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------------------------------------
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The Firedrake Team will be delivering a finite element course, with practical
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examples in Firedrake (of course!) at the `African Institute for Mathematical
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Sciences Rwanda <https://aims.ac.rw>`__ from 8 to 12 April 2025.
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Course programme
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----------------
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The course will draw heavily on the materials for a `finite element course
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taught at Imperial College London <https://finite-element.github.io>`__ and the
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`Firedrake manual
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<https://www.firedrakeproject.org/documentation.html#manual>`__.
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The materials most relevant for each section are linked below, but further
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reading is available on the links above.
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.. list-table::
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* -
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- **Tuesday**
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- **Wednesday**
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- **Thursday**
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- **Friday**
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- **Saturday**
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* - **Early AM**
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- `Function spaces and inner products <https://wp.doc.ic.ac.uk/spo/wp-content/uploads/sites/31/2013/11/notes.pdf>`__
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- `The Ciarlet finite element <https://finite-element.github.io/L2_fespaces.html>`__
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- `Nonlinear problems <https://finite-element.github.io/8_nonlinear_problems.html>`__
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- Devito: inverse tomography
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- Software for adjoints: differentiable programming
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* - **Late AM**
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- `Our first finite element problem <https://finite-element.github.io/L1_introduction.html>`__
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- Firedrake practical 3: `vector-valued problems <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/03-elasticity.ipynb>`__
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- Firedrake practical 5: `The Burgers equation <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/04-burgers.ipynb>`__
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- Adjoints part 1: `derivation <https://www.firedrakeproject.org/adjoint.html>`__
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- Adjoint practical 2: the tape
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* - **Early PM**
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- Firedrake practical 1: `Helmholtz Equation <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/01-spd-helmholtz.ipynb>`__
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- `Systems with more than one variable <https://finite-element.github.io/9_mixed_problems.html>`__
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- An introduction to solvers and preconditioners
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- Devito: inverse tomography
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- `Deep learning introduction <https://github.com/NBoulle/physics-driven-ml/raw/main/tutorials/intro_deep_learning.pdf>`__, `practical <https://colab.research.google.com/github/NBoulle/physics-driven-ml/blob/main/tutorials/Tutorial_1_ex.ipynb>`__
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* - **Late PM**
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- Firedrake practical 2: `Dirichlet boundary conditions <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/02-poisson.ipynb>`__
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- Firedrake practical 4: `mixed Poisson <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/05-mixed-poisson.ipynb>`__
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- Firedrake practical 6: `solvers <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/08-composable-solvers.ipynb>`__
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- Adjoint practical 1: Burgers again
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- `Scientific machine learning <https://github.com/NBoulle/physics-driven-ml/raw/main/tutorials/sciml_intro.pdf>`__, `practical <https://colab.research.google.com/github/NBoulle/physics-driven-ml/blob/main/tutorials/Tutorial_2_ex.ipynb>`__
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Course lecturers
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----------------
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* `David Ham <https://profiles.imperial.ac.uk/david.ham>`__, Department of Mathematics, Imperial College London
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* `Nicolas Boullé <https://profiles.imperial.ac.uk/n.boulle>`__, Department of Mathematics, Imperial College London
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* `Jack Betteridge <https://www.devitocodes.com/about/#jack-betteridge-research-scientist>`__, Devito Codes and Department of Mathematics, Imperial College London
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‎docs/source/events.rst‎

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downstream applications. For more details see `the website
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<https://ccp-dcm.github.io/exeter_hackathon.html>`__.
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Finite Element Course at AIMS Rwanda
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The Firedrake team will be presenting a short course on the Finite Element
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Method at the African Institute for Mathematical Sciences in Kigali between 8
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and 12 April 2025. For more information see :doc:`the course page <aims_25>`.
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Firedrake USA'25
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~~~~~~~~~~~~~~~~
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‎docs/source/visualisation.rst‎

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Output for visualisation purposes is managed with a
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:class:`~.vtk_output.VTKFile` object. To create one, first import the
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class from `firedrake.output, then we just need to pass the name of the
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output file on disk. The file Firedrake creates is in PVD_ and
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output file on disk. The file Firedrake creates is in PVD and
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therefore the requested file name must end in ``.pvd``.
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.. code-block:: python3
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t += dt
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The PVD_ data format supports specifying the timestep value for
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The PVD data format supports specifying the timestep value for
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time-dependent data. We do not have to provide it to
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:meth:`~.vtk_output.VTKFile.write`, by default an integer counter is
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used that is incremented by 1 each time
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.. _Paraview: http://www.paraview.org
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.. _VTK: http://www.vtk.org
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.. _PVD: http://www.paraview.org/Wiki/ParaView/Data_formats#PVD_File_Format
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.. _matplotlib: http://matplotlib.org
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.. _Arbitrary: https://www.kitware.com/modeling-arbitrary-order-lagrange-finite-elements-in-the-visualization-toolkit/
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__ Arbitrary_

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