Merge branch 'main' of github.com:NDF-Poli-USP/spyro into issue_0123-…

…add-fwi-tutorial-and-more-test-cases

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Run lint
+
+on:
+  # Push to master or PR
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  linter:
+    name: "Run linter"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+      - name: Setup flake8 annotations
+        uses: rbialon/flake8-annotations@v1
+      - name: Install linter
+        run: |
+          pip install flake8 pylint
+      - name: Lint codebase
+        run: |
+          make lint GITHUB_ACTIONS_FORMATTING=1

.github/workflows/python-tests.yml

@@ -17,11 +17,11 @@ jobs:
     - uses: actions/checkout@v3
     - name: Running serial tests
       run: |
-          source /home/olender/firedrakes/2024_07_19/firedrake/bin/activate
+          source /home/olender/firedrakes/2024_09_11/firedrake/bin/activate
           pytest --cov-report=xml --cov=spyro test/
     - name: Running parallel 3D forward test
       run: |
-          source /home/olender/firedrakes/2024_07_19/firedrake/bin/activate
+          source /home/olender/firedrakes/2024_09_11/firedrake/bin/activate
           mpiexec -n 6 pytest test_3d/test_hexahedral_convergence.py
           mpiexec -n 6 pytest test_parallel/test_forward.py
           mpiexec -n 6 pytest test_parallel/test_fwi.py
@@ -33,17 +33,17 @@ jobs:
     - name: Covering parallel 3D forward test
       continue-on-error: true
       run: |
-          source /home/olender/firedrakes/2024_07_19/firedrake/bin/activate
+          source /home/olender/firedrakes/2024_09_11/firedrake/bin/activate
           mpiexec -n 6 pytest --cov-report=xml --cov-append --cov=spyro test_3d/test_hexahedral_convergence.py
     - name: Covering parallel forward test
       continue-on-error: true
       run: |
-          source /home/olender/firedrakes/2024_07_19/firedrake/bin/activate
+          source /home/olender/firedrakes/2024_09_11/firedrake/bin/activate
           mpiexec -n 6 pytest --cov-report=xml --cov-append --cov=spyro test_parallel/test_forward.py
     - name: Covering parallel fwi test
       continue-on-error: true
       run: |
-          source /home/olender/firedrakes/2024_07_19/firedrake/bin/activate
+          source /home/olender/firedrakes/2024_09_11/firedrake/bin/activate
           mpiexec -n 6 pytest --cov-report=xml --cov-append --cov=spyro test_parallel/test_fwi.py
     - name: Covering parallel supershot test
       continue-on-error: true
@@ -71,5 +71,5 @@ jobs:
           source /home/olender/firedrakes/2024_07_19/firedrake/bin/activate
           mpiexec -n 2 pytest --cov-report=xml --cov-append --cov=spyro test_parallel/test_test_gradient_serialshots.py
     - name: Uploading coverage to Codecov
-      run: export CODECOV_TOKEN="057ec853-d7ea-4277-819b-0c5ea2f9ff57" && bash <(curl -s https://codecov.io/bash)
+      run: export CODECOV_TOKEN="6cd21147-54f7-4b77-94ad-4b138053401d" && bash <(curl -s https://codecov.io/bash)
 

.gitignore

@@ -7,3 +7,5 @@
 *.hdf5
 *.msh
 *.segy
+*.png
+*.vtk

Makefile

@@ -25,13 +25,7 @@ clean:
 	@rm -rf dist/
 
 format:
-	isort -rc spyro/ test/*.py
-	black spyro/ test/*.py
-
-black:
-	black .
+	autopep8 --in-place --global-config setup.cfg --recursive .
 
 lint:
-	isort --check . spyro/ setup.py test/*.py
-	black --check spyro/ setup.py test/*.py
 	flake8 setup.py spyro/ test/*.py

README.md

@@ -1,6 +1,6 @@
 [![DOI](https://zenodo.org/badge/318542339.svg)](https://zenodo.org/badge/latestdoi/318542339)
 [![Python tests](https://github.com/NDF-Poli-USP/spyro/actions/workflows/python-tests.yml/badge.svg)](https://github.com/NDF-Poli-USP/spyro/actions/workflows/python-tests.yml)
-[![codecov](https://codecov.io/gh/Olender/spyro-1/graph/badge.svg?token=69M30UMRFD)](https://codecov.io/gh/Olender/spyro-1)
+[![codecov](https://codecov.io/gh/NDF-Poli-USP/spyro/graph/badge.svg?token=8NM4N4N7YW)](https://codecov.io/gh/NDF-Poli-USP/spyro)
 
 spyro: seismic parallel inversion and reconstruction optimization framework
 ============================================

demos/with_automatic_differentiation/run_forward_ad.py

@@ -0,0 +1,46 @@
+import firedrake as fire
+import spyro
+from demos.with_automatic_differentiation.utils import \
+    model_settings, make_c_camembert
+import os
+os.environ["OMP_NUM_THREADS"] = "1"
+
+# --- Basid setup to run a forward simulation with AD --- #
+
+model = model_settings()
+
+# Use emsemble parallelism.
+M = model["parallelism"]["num_spacial_cores"]
+my_ensemble = fire.Ensemble(fire.COMM_WORLD, M)
+mesh = fire.UnitSquareMesh(50, 50, comm=my_ensemble.comm)
+element = fire.FiniteElement(
+    model["opts"]["method"], mesh.ufl_cell(), degree=model["opts"]["degree"],
+    variant=model["opts"]["quadrature"]
+)
+V = fire.FunctionSpace(mesh, element)
+
+
+forward_solver = spyro.solvers.forward_ad.ForwardSolver(model, mesh, V)
+
+c_true = make_c_camembert(mesh, V)
+# Ricker wavelet
+wavelet = spyro.full_ricker_wavelet(
+    model["timeaxis"]["dt"], model["timeaxis"]["tf"],
+    model["acquisition"]["frequency"],
+)
+
+if model["parallelism"]["type"] is None:
+    outfile = fire.VTKFile("solution.pvd")
+    for sn in range(len(model["acquisition"]["source_pos"])):
+        rec_data, _ = forward_solver.execute(c_true, sn, wavelet)
+        sol = forward_solver.solution
+        outfile.write(sol)
+else:
+    # source_number based on the ensemble.ensemble_comm.rank
+    source_number = my_ensemble.ensemble_comm.rank
+    rec_data, _ = forward_solver.execute_acoustic(
+        c_true, source_number, wavelet)
+    sol = forward_solver.solution
+    fire.VTKFile(
+        "solution_" + str(source_number) + ".pvd", comm=my_ensemble.comm
+    ).write(sol)

demos/with_automatic_differentiation/run_fwi_ad.py

@@ -0,0 +1,112 @@
+import firedrake as fire
+import firedrake.adjoint as fire_ad
+from checkpoint_schedules import Revolve
+import spyro
+from demos.with_automatic_differentiation import utils
+import os
+os.environ["OMP_NUM_THREADS"] = "1"
+
+# --- Basid setup to run a FWI --- #
+model = utils.model_settings()
+
+
+def forward(
+        c, compute_functional=False, true_data_receivers=None, annotate=False
+):
+    """Time-stepping acoustic forward solver.
+
+    The time integration is done using a central difference scheme.
+
+    Parameters
+    ----------
+    c : firedrake.Function
+        Velocity field.
+    compute_functional : bool, optional
+        Whether to compute the functional. If True, the true receiver
+        data must be provided.
+    true_data_receivers : list, optional
+        True receiver data. This is used to compute the functional.
+    annotate : bool, optional
+        If True, the forward model is annotated for automatic differentiation.
+
+    Returns
+    -------
+    (receiver_data : list, J_val : float)
+        Receiver data and functional value.
+    """
+    if annotate:
+        fire_ad.continue_annotation()
+        if model["aut_dif"]["checkpointing"]:
+            total_steps = int(model["timeaxis"]["tf"] / model["timeaxis"]["dt"])
+            steps_store = int(total_steps / 10)  # Store 10% of the steps.
+            tape = fire_ad.get_working_tape()
+            tape.progress_bar = fire.ProgressBar
+            tape.enable_checkpointing(Revolve(total_steps, steps_store))
+
+    if model["parallelism"]["type"] is None:
+        outfile = fire.VTKFile("solution.pvd")
+        receiver_data = []
+        J = 0.0
+        for sn in range(len(model["acquisition"]["source_pos"])):
+            rec_data, J_val = forward_solver.execute_acoustic(c, sn, wavelet)
+            receiver_data.append(rec_data)
+            J += J_val
+            sol = forward_solver.solution
+            outfile.write(sol)
+
+    else:
+        # source_number based on the ensemble.ensemble_comm.rank
+        source_number = my_ensemble.ensemble_comm.rank
+        receiver_data, J = forward_solver.execute_acoustic(
+            c, source_number, wavelet,
+            compute_functional=compute_functional,
+            true_data_receivers=true_data_receivers
+        )
+        sol = forward_solver.solution
+        fire.VTKFile(
+            "solution_" + str(source_number) + ".pvd", comm=my_ensemble.comm
+        ).write(sol)
+
+    return receiver_data, J
+
+
+# Use emsemble parallelism.
+M = model["parallelism"]["num_spacial_cores"]
+my_ensemble = fire.Ensemble(fire.COMM_WORLD, M)
+mesh = fire.UnitSquareMesh(50, 50, comm=my_ensemble.comm)
+element = fire.FiniteElement(
+    model["opts"]["method"], mesh.ufl_cell(), degree=model["opts"]["degree"],
+    variant=model["opts"]["quadrature"]
+)
+V = fire.FunctionSpace(mesh, element)
+
+
+forward_solver = spyro.solvers.forward_ad.ForwardSolver(model, mesh, V)
+# Camembert model.
+c_true = utils.make_c_camembert(mesh, V)
+# Ricker wavelet
+wavelet = spyro.full_ricker_wavelet(
+    model["timeaxis"]["dt"], model["timeaxis"]["tf"],
+    model["acquisition"]["frequency"],
+)
+
+true_rec, _ = forward(c_true)
+
+# --- FWI with AD --- #
+c_guess = utils.make_c_camembert(mesh, V, c_guess=True)
+guess_rec, J = forward(
+    c_guess, compute_functional=True, true_data_receivers=true_rec,
+    annotate=True
+)
+
+# :class:`~.EnsembleReducedFunctional` is employed to recompute in
+# parallel the functional and its gradient associated with the multiple sources
+# (3 in this case).
+J_hat = fire_ad.EnsembleReducedFunctional(
+    J, fire_ad.Control(c_guess), my_ensemble)
+c_optimised = fire_ad.minimize(J_hat, method="L-BFGS-B",
+                               options={"disp": True, "maxiter": 10},
+                               bounds=(1.5, 3.5),
+                               derivative_options={"riesz_representation": 'l2'})
+
+fire.VTKFile("c_optimised.pvd").write(c_optimised)

demos/with_automatic_differentiation/utils.py

@@ -0,0 +1,105 @@
+# --- Basid setup to run a forward simulation with AD --- #
+import firedrake as fire
+import spyro
+
+
+def model_settings():
+    """Model settings for forward and Full Waveform Inversion (FWI)
+    simulations.
+
+    Returns
+    -------
+    model : dict
+        Dictionary containing the model settings.
+    """
+
+    model = {}
+
+    model["opts"] = {
+        "method": "KMV",  # either CG or mass_lumped_triangle
+        "quadrature": "KMV",  # Equi or mass_lumped_triangle
+        "degree": 1,  # p order
+        "dimension": 2,  # dimension
+        "regularization": False,  # regularization is on?
+        "gamma": 1e-5,  # regularization parameter
+    }
+
+    model["parallelism"] = {
+        # options:
+        # `shots_parallelism`. Shots parallelism.
+        # None - no shots parallelism.
+        "type": "shots_parallelism",
+        "num_spacial_cores": 1,  # Number of cores to use in the spatial
+        # parallelism.
+    }
+
+    # Define the domain size without the ABL.
+    model["mesh"] = {
+        "Lz": 1.0,  # depth in km - always positive
+        "Lx": 1.0,  # width in km - always positive
+        "Ly": 0.0,  # thickness in km - always positive
+        "meshfile": "not_used.msh",
+        "initmodel": "not_used.hdf5",
+        "truemodel": "not_used.hdf5",
+    }
+
+    # Specify a 250-m Absorbing Boundary Layer (ABL) on the three sides of the domain to damp outgoing waves.
+    model["BCs"] = {
+        "status": False,  # True or False, used to turn on any type of BC
+        "outer_bc": "non-reflective",  # none or non-reflective (outer boundary condition)
+        "abl_bc": "none",  # none, gaussian-taper, or alid
+        "lz": 0.0,  # thickness of the ABL in the z-direction (km) - always positive
+        "lx": 0.0,  # thickness of the ABL in the x-direction (km) - always positive
+        "ly": 0.0,  # thickness of the ABL in the y-direction (km) - always positive
+    }
+
+    model["acquisition"] = {
+        "source_type": "Ricker",
+        "source_pos": spyro.create_transect((0.2, 0.15), (0.8, 0.15), 3),
+        "frequency": 7.0,
+        "delay": 1.0,
+        "receiver_locations": spyro.create_transect((0.2, 0.2), (0.8, 0.2), 10),
+    }
+    model["aut_dif"] = {
+        "status": True,
+        "checkpointing": True,
+    }
+
+    model["timeaxis"] = {
+        "t0": 0.0,  # Initial time for event
+        "tf": 0.8,  # Final time for event (for test 7)
+        "dt": 0.001,  # timestep size (divided by 2 in the test 4. dt for test 3 is 0.00050)
+        "amplitude": 1,  # the Ricker has an amplitude of 1.
+        "nspool": 20,  # (20 for dt=0.00050) how frequently to output solution to pvds
+        "fspool": 1,  # how frequently to save solution to RAM
+    }
+
+    return model
+
+
+def make_c_camembert(mesh, function_space, c_guess=False, plot_c=False):
+    """Acoustic velocity model.
+
+    Parameters
+    ----------
+    mesh : firedrake.Mesh
+        Mesh.
+    function_space : firedrake.FunctionSpace
+        Function space.
+    c_guess : bool, optional
+        If True, the initial guess for the velocity field is returned.
+    plot_c : bool, optional
+        If True, the velocity field is saved to a VTK file.
+    """
+    x, z = fire.SpatialCoordinate(mesh)
+    if c_guess:
+        c = fire.Function(function_space).interpolate(1.5 + 0.0 * x)
+    else:
+        c = fire.Function(function_space).interpolate(
+            2.5
+            + 1 * fire.tanh(100 * (0.125 - fire.sqrt((x - 0.5) ** 2 + (z - 0.5) ** 2)))
+        )
+    if plot_c:
+        outfile = fire.VTKFile("acoustic_cp.pvd")
+        outfile.write(c)
+    return c