Adjoint inverse reconstruction¶
Introduction¶
In this tutorial, we will demonstrate how to perform an inversion to recover the initial temperature field of an idealised mantle convection simulation using G-ADOPT. This tutorial is published as the first synthetic experiment in Ghelichkhan et al. (2024). The full inversion showcased in the publication involves a total number of 80 timesteps. For the tutorial here we start with only 5 timesteps to go through the basics.
The tutorial involves a twin experiment, where we assess the performance of the inversion scheme by inverting the initial state of a synthetic reference simulation, known as the "Reference Twin". To create this reference twin, we run a forward mantle convection simulation and record all relevant fields (velocity and temperature) at each time step.
We have pre-run this simulation by running the forward case, and stored model output as a checkpoint file on our servers. These fields serve as benchmarks for evaluating our inverse problem's performance. To download the reference benchmark checkpoint file if it doesn't already exist, execute the following command:
![ ! -f adjoint-demo-checkpoint-state.h5 ] && wget https://data.gadopt.org/demos/adjoint-demo-checkpoint-state.h5
In this file, fields from the reference simulation are stored under the names "Temperature" and "Velocity". After importing g-adopt and the associated inverse module (gadopt.inverse - discussed further below), we can retrieve timestepping information from the pre-computed forward run as follows
from gadopt import *
from gadopt.inverse import *
# Open the checkpoint file and subsequently load the mesh:
checkpoint_filename = "adjoint-demo-checkpoint-state.h5"
checkpoint_file = CheckpointFile(checkpoint_filename, mode="r")
mesh = checkpoint_file.load_mesh("firedrake_default_extruded")
mesh.cartesian = True
# Specify boundary markers, noting that for extruded meshes the upper and lower boundaries are tagged as
# "top" and "bottom" respectively.
boundary = get_boundary_ids(mesh)
# Retrieve the timestepping information for the Velocity and Temperature functions from checkpoint file:
temperature_timestepping_info = checkpoint_file.get_timestepping_history(mesh, "Temperature")
velocity_timestepping_info = checkpoint_file.get_timestepping_history(mesh, "Velocity")
We can check the information for each:
print("Timestepping info for Temperature", temperature_timestepping_info)
print("Timestepping info for Velocity", velocity_timestepping_info)
Timestepping info for Temperature {'index': array([ 0., 79.])}
Timestepping info for Velocity {'index': array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12.,
13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25.,
26., 27., 28., 29., 30., 31., 32., 33., 34., 35., 36., 37., 38.,
39., 40., 41., 42., 43., 44., 45., 46., 47., 48., 49., 50., 51.,
52., 53., 54., 55., 56., 57., 58., 59., 60., 61., 62., 63., 64.,
65., 66., 67., 68., 69., 70., 71., 72., 73., 74., 75., 76., 77.,
78., 79.]), 'delta_t': array([4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06,
4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06, 4.e-06])}
The timestepping information reveals that there are 80 time-steps (from 0 to 79) in the reference simulation, with the temperature field stored only at the initial (index=0) and final (index=79) timesteps, while the velocity field is stored at all timesteps. We can visualise the benchmark fields using Firedrake's built-in VTK functionality. For example, initial and final temperature fields can be loaded:
# Load the final state, analagous to the present-day "observed" state:
Tobs = checkpoint_file.load_function(mesh, "Temperature", idx=int(temperature_timestepping_info["index"][-1]))
Tobs.rename("Observed Temperature")
# Load the reference initial state - i.e. the state that we wish to recover:
Tic_ref = checkpoint_file.load_function(mesh, "Temperature", idx=int(temperature_timestepping_info["index"][0]))
Tic_ref.rename("Reference Initial Temperature")
checkpoint_file.close()
These fields can be visualised using standard VTK software, such as Paraview or pyvista.
import pyvista as pv
VTKFile("./visualisation_vtk.pvd").write(Tobs, Tic_ref)
dataset = pv.read('./visualisation_vtk.pvd')
# Create a plotter object
plotter = pv.Plotter()
# Add the dataset to the plotter
plotter.add_mesh(dataset, scalars='Observed Temperature', cmap='coolwarm')
# Adjust the camera position
plotter.camera_position = [(0.5, 0.5, 2.5), (0.5, 0.5, 0), (0, 1, 0)]
# Show the plot
plotter.show(jupyter_backend="static")
The Inverse Code¶
The novelty of using the overloading approach provided by pyadjoint is that it requires minimal changes to our script to enable the inverse capabalities of G-ADOPT. To turn on the adjoint, one simply imports the inverse module (already done above) to enable all taping functionality from pyadjoint.
Doing so will turn Firedrake's objects to overloaded types, in a way that any UFL operation will be annotated and added to the tape, unless otherwise specified.
We first ensure that the tape is cleared of any previous operations, using the following code:
tape = get_working_tape()
tape.clear_tape()
# To verify the tape is empty, we can print all blocks:
print(tape.get_blocks())
[]
From here on, all user operations are specified with minimal differences relative to to our forward code. Under the hood, however, the tape will be populated by blocks that record their dependencies. Knowing the mesh was loaded above, we continue in a manner that is consistent with our most basic forward modelling tutorials.
# Set up function spaces:
V = VectorFunctionSpace(mesh, "CG", 2) # Velocity function space (vector)
W = FunctionSpace(mesh, "CG", 1) # Pressure function space (scalar)
Q = FunctionSpace(mesh, "DQ", 2) # Temperature function space (DQ; scalar)
Z = MixedFunctionSpace([V, W]) # Mixed function space
# Specify test functions and functions to hold solutions:
z = Function(Z) # A field over the mixed function space Z
u, p = split(z) # Returns symbolic UFL expression for u and p
z.subfunctions[0].rename("Velocity")
z.subfunctions[1].rename("Pressure")
T = Function(Q, name="Temperature")
# Specify important constants for the problem, alongside the approximation:
Ra = Constant(1e6) # Rayleigh number
approximation = BoussinesqApproximation(Ra)
# Define time-stepping parameters:
delta_t = Constant(4e-6) # Constant time step
timesteps = int(temperature_timestepping_info["index"][-1]) + 1 # number of timesteps from forward
# Nullspaces for the problem are next defined:
Z_nullspace = create_stokes_nullspace(Z, closed=True, rotational=False)
# Followed by boundary conditions, noting that all boundaries are free slip, whilst the domain is
# heated from below (T = 1) and cooled from above (T = 0).
stokes_bcs = {
boundary.bottom: {"uy": 0},
boundary.top: {"uy": 0},
boundary.left: {"ux": 0},
boundary.right: {"ux": 0},
}
temp_bcs = {
boundary.bottom: {"T": 1.0},
boundary.top: {"T": 0.0},
}
# Setup Energy and Stokes solver
energy_solver = EnergySolver(T, u, approximation, delta_t, ImplicitMidpoint, bcs=temp_bcs)
stokes_solver = StokesSolver(
z,
approximation,
T,
bcs=stokes_bcs,
nullspace=Z_nullspace,
transpose_nullspace=Z_nullspace,
)
Specify Problem Length¶
For the purpose of this demo, we only invert for a total of 10 time-steps. This makes it tractable to run this within a tutorial session.
To run for the simulation's full duration, change the initial_timestep to 0 below, rather than
timesteps - 10.
initial_timestep = timesteps - 10
Define the Control Space¶
In this section, we define the control space, which can be restricted to reduce the risk of encountering an
undetermined problem. Here, we select the Q1 function space for the initial condition $T_{ic}$. We also provide an
initial guess for the control value, which in this synthetic test is the temperature field of the reference
simulation at the final time-step (timesteps - 1). In other words, our guess for the initial temperature
is the final model state.
# Define control function space:
Q1 = FunctionSpace(mesh, "CG", 1)
# Create a function for the unknown initial temperature condition, which we will be inverting for. Our initial
# guess is set to the 1-D average of the forward model. We first load that, at the relevant timestep.
# Note that this layer average will later be used for the smoothing term in our objective functional.
with CheckpointFile(checkpoint_filename, mode="r") as checkpoint_file:
Taverage = checkpoint_file.load_function(mesh, "Average_Temperature", idx=initial_timestep)
Tic = Function(Q1, name="Initial_Condition_Temperature").assign(Taverage)
# Given that Tic will be updated during the optimisation, we also create a function to store our initial guess,
# which we will later use for smoothing. Note that since smoothing is executed in the control space, we must
# specify boundary conditions on this term in that same Q1 space.
T0_bcs = [DirichletBC(Q1, 0., boundary.top), DirichletBC(Q1, 1., boundary.bottom)]
T0 = Function(Q1, name="Initial_Guess_Temperature").project(Tic, bcs=T0_bcs)
# We next make pyadjoint aware of our control problem:
control = Control(Tic)
# Take our initial guess and project to T, simultaneously applying boundary conditions in the Q2 space:
T.project(Tic, bcs=energy_solver.strong_bcs)
# We continue by integrating the solutions at each time-step.
# Notice that we cumulatively compute the misfit term with respect to the
# surface velocity observable.
Coefficient(WithGeometry(FunctionSpace(<firedrake.mesh.ExtrudedMeshTopology object at 0x77946c931e50>, TensorProductElement(FiniteElement('Discontinuous Lagrange', interval, 2), FiniteElement('Discontinuous Lagrange', interval, 2), cell=TensorProductCell(interval, interval)), name=None), Mesh(VectorElement(TensorProductElement(FiniteElement('Lagrange', interval, 1), FiniteElement('Lagrange', interval, 1), cell=TensorProductCell(interval, interval)), dim=2), 1)), 32)
u_misfit = 0.0
# Next populate the tape by running the forward simulation.
for time_idx in range(initial_timestep, timesteps):
stokes_solver.solve()
energy_solver.solve()
# Update the accumulated surface velocity misfit using the observed value.
with CheckpointFile(checkpoint_filename, mode="r") as checkpoint_file:
uobs = checkpoint_file.load_function(mesh, name="Velocity", idx=time_idx)
u_misfit += assemble(dot(u - uobs, u - uobs) * ds_t)
Define the Objective Functional¶
Now that all calculations are in place, we must define the objective functional. The objective functional is our way of expressing our goal for this optimisation. It is composed of several terms, each representing a different aspect of the model's performance and regularisation.
Regularisation involves imposing constraints on solutions to prevent overfitting, ensuring that the model
generalises well to new data. In this context, we use the one-dimensional (1-D) temperature profile derived from
the reference simulation as our regularisation constraint. This profile, referred to below as Taverage, helps
stabilise the inversion process by providing a benchmark that guides the solution towards physically plausible states.
We use Taverage as a part of the damping and smoothing terms in our regularisation.
Consequently, the complete objective functional is defined mathematically as follows:
Reiterating that:
- $T_{ic}$ is the initial temperature condition.
- $T_{\text{average}}$ is the average temperature profile representing mantle's geotherm.
- $T_{F}$ is the the temperature field at final time-step.
- $T_{\text{obs}}$ is the observed temperature field at the final time-step.
- $u_{\text{obs}}$ is the observed velocity field at each time-step.
- $\alpha_u$, $\alpha_d$, $\alpha_s$ are the three different weighting terms for the velocity, damping and smoothing terms.
We define the objective functional as $$ \text{Objective Functional}= \int_{\Omega}(T - T_{\text{obs}}) ^ 2 \, dx \\ +\alpha_u\, \frac{D_{T_{obs}}}{N\times D_{u_{obs}}}\sum_{i}\int_{\partial \Omega_{\text{top}}}(u - u_{\text{obs}}) \cdot(u - u_{\text{obs}}) \, ds \\ +\alpha_s\, \frac{D_{T_{obs}}}{D_{\text{smoothing}}}\int_{\Omega} \nabla(T_{ic} - T_{\text{average}}) \cdot \nabla(T_{ic} - T_{\text{average}}) \, dx \\ +\alpha_d\, \frac{D_{T_{obs}}}{D_{\text{damping}}}\int_{\Omega}(T_{ic} - T_{\text{average}}) ^ 2 \, dx $$
With the three normlisation terms of:
- $D_{\text{damping}} = \int_{\Omega} T_{\text{average}}^2 \, dx$,
- $D_{\text{smoothing}} = \int_{\Omega} \nabla T_{\text{obs}} \cdot \nabla T_{\text{obs}} \, dx$,
- $D_{T_{obs}} = \int_{\Omega} T_{\text{obs}} ^ 2 \, dx$, and
- $D_{\text{damping}} = \int_{\partial \Omega_{\text{top}}} u_{\text{obs}} \cdot u_{\text{obs}} \, ds$
which we specify through the objective below:
# Define component terms of overall objective functional and their normalisation terms:
damping = assemble((T0 - Taverage) ** 2 * dx)
norm_damping = assemble(Taverage**2 * dx)
smoothing = assemble(dot(grad(T0 - Taverage), grad(T0 - Taverage)) * dx)
norm_smoothing = assemble(dot(grad(Tobs), grad(Tobs)) * dx)
norm_obs = assemble(Tobs**2 * dx)
norm_u_surface = assemble(dot(uobs, uobs) * ds_t)
# Define temperature misfit between final state solution and observation:
t_misfit = assemble((T - Tobs) ** 2 * dx)
# Weighting terms
alpha_u = 1e-1
alpha_d = 1e-3
alpha_s = 1e-3
# Define overall objective functional:
objective = (
t_misfit +
alpha_u * (norm_obs * u_misfit / timesteps / norm_u_surface) +
alpha_d * (norm_obs * damping / norm_damping) +
alpha_s * (norm_obs * smoothing / norm_smoothing)
)
Define the Reduced Functional¶
In optimisation terminology, a reduced functional is a functional that takes a given value for the control and outputs the value of the objective functional defined for it. It does this without explicitly depending on all intermediary state variables, hence the name "reduced".
To define the reduced functional, we provide the class with an objective (which is an overloaded UFL object) and the control.
reduced_functional = ReducedFunctional(objective, control)
At this point, we have completed annotating the tape with the necessary information from running the forward simulation. To prevent further annotations during subsequent operations, we stop the annotation process. This ensures that no additional solves are unnecessarily recorded, keeping the tape focused only on the essential steps.
pause_annotation()
We can print the contents of the tape at this stage to verify that it is not empty.
print(tape.get_blocks())
[<firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440408fb0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404096d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440409850>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x77944040aab0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x77944040bd70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440484650>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440484770>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x77944040b230>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440371730>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x779440372630>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x779440372e70>, <firedrake.adjoint_utils.blocks.solving.ProjectBlock object at 0x779440372570>, <firedrake.adjoint_utils.blocks.solving.ProjectBlock object at 0x77946a6f29f0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x77946a6f3590>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x77944030fbf0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7794404eebd0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7794404ef410>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x77944030fc50>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440357950>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404d19d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404d2db0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404d1f70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404d0d10>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404d29f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404d0e90>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404d0650>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7794404d0410>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x77944033bd70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404ed5b0>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x779440357e30>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77944030e570>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13e270>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13f5f0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13c950>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13f170>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x77944030fd70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x77944030e2d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13e570>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13e930>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13f710>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13e210>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13d8b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13f230>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13ee10>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc13eb70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13c650>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13fb90>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc13c7d0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793dc13cad0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13f650>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13fb30>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13d910>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13cfb0>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc13d7f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13d4f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13f7d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13f110>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13f830>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13c3b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13dbb0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13e8d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13d0d0>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc13e810>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d51f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d5a90>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc2d5130>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793dc2d4890>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d6030>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d4dd0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d7470>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d7050>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc2d7cb0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d6570>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d62d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d7530>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d52b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d73b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d5fd0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d7170>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d4f50>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc2d4b30>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d7950>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d6510>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc13ce30>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793dc13f770>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc13ee70>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c46382f0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c4638e90>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c4638a10>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc13daf0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc13c230>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c4638a70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c46385f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c463a570>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c4638350>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c463bef0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c463abd0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c463b470>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793c463a9f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440355fd0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440356030>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc2d5490>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x779440357230>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d6270>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d7a70>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d7fb0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2d4170>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7794403568d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2d64b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x779440356db0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465e930>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465e8d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465ed50>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465e1b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465e4b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465ea50>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793c465e150>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465c9b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465d8b0>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793c465ee10>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793c465d970>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c465eed0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c465f2f0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c465ee70>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c465f0b0>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793c465cef0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465e690>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465c4d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465da90>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465f290>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465dfd0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465e570>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465f230>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465f170>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793c465cfb0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465f830>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c465fd70>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc2e00b0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793dc2e3b90>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e21b0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e2ff0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e1970>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e1d90>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc2e3fb0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e2510>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e39b0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e2810>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e2f30>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e0b30>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e1df0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e3230>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e0350>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc2e3170>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e2870>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e2e70>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc2e33b0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793dc2e2750>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e1a90>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e26f0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e0410>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793dc2e0f50>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc2e1b50>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e0590>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e23f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e0770>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e0ef0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e3110>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e37d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e2990>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793dc2e0530>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793dc2e13d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404ab770>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404a9bb0>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7794404aa810>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7794404a8fb0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7794404a9eb0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c43b8dd0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c43ba5d0>, <firedrake.adjoint_utils.blocks.dirichlet_bc.DirichletBCBlock object at 0x7793c43b9e50>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7794404a96d0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7794404a94f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43b9190>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43bb110>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43ba630>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43b9fd0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43ba390>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43ba0f0>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43b8a10>, <firedrake.adjoint_utils.blocks.solving.NonlinearVariationalSolveBlock object at 0x7793c43bbd70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43bba70>, <firedrake.adjoint_utils.blocks.function.FunctionAssignBlock object at 0x7793c43b8d70>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793c43bb470>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793c43b8b90>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc11ecf0>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc11cbf0>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc2d7710>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793dc2e0dd0>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x77942c68e690>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x7793c465d370>, <firedrake.adjoint_utils.blocks.assembly.AssembleBlock object at 0x77942c68c410>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x7793dc2d4770>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68cb30>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68d190>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68ebd0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68fd70>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68f7d0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68eab0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68fad0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68f530>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77942c68d8b0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77944045c470>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77944045d2b0>, <pyadjoint.adjfloat.AdjFloatExprBlock object at 0x77944045edb0>]
Verification of Gradients: Taylor Remainder Convergence Test¶
A fundamental tool for verifying gradients is the Taylor remainder convergence test. This test helps ensure that the gradients computed by our optimisation algorithm are accurate. For the reduced functional, $J(T_{ic})$, and its derivative, $\frac{\mathrm{d} J}{\mathrm{d} T_{ic}}$, the Taylor remainder convergence test can be expressed as:
$$ \left| J(T_{ic} + h \,\delta T_{ic}) - J(T_{ic}) - h\,\frac{\mathrm{d} J}{\mathrm{d} T_{ic}} \cdot \delta T_{ic} \right| \longrightarrow 0 \text{ at } O(h^2). $$
The expression on the left-hand side is termed the second-order Taylor remainder. This term's convergence rate of $O(h^2)$ is a robust indicator for verifying the computational implementation of the gradient calculation. Essentially, if you halve the value of $h$, the magnitude of the second-order Taylor remainder should decrease by a factor of 4.
We employ these so-called Taylor tests to confirm the accuracy of the determined gradients. The theoretical convergence rate is $O(2.0)$, and achieving this rate indicates that the gradient information is accurate down to floating-point precision.
Performing Taylor Tests¶
In our implementation, we perform a second-order Taylor remainder test for each term of the objective functional. The test involves computing the functional and the associated gradient when randomly perturbing the initial temperature field, $T_{ic}$, and subsequently halving the perturbations at each level.
Here is how you can perform a Taylor test in the code:
# Define the perturbation in the initial temperature field
import numpy as np
Delta_temp = Function(Tic.function_space(), name="Delta_Temperature")
Delta_temp.dat.data[:] = np.random.random(Delta_temp.dat.data.shape)
# Perform the Taylor test to verify the gradients
minconv = taylor_test(reduced_functional, Tic, Delta_temp)
Running Taylor test
Computed residuals: [4.979642597106596e-05, 1.2449106537244113e-05, 3.112276639930322e-06, 7.78069160623823e-07] Computed convergence rates: [1.9999999948456022, 1.9999999973951779, 1.9999999988110089]
The taylor_test function computes the Taylor remainder and verifies that the convergence rate is close to the theoretical value of $O(2.0)$. This ensures
that our gradients are accurate and reliable for optimisation.
Running the inversion¶
In the final section of this tutorial, we run the optimisation method. First, we define lower and upper bounds for the optimisation problem to guide the optimisation method towards a more constrained solution.
For this simple problem, we perform a bounded nonlinear optimisation where the temperature is only permitted to lie in the range [0, 1]. This means that the optimisation problem should not search for solutions beyond these values.
# Define lower and upper bounds for the temperature
T_lb = Function(Tic.function_space(), name="Lower Bound Temperature")
T_ub = Function(Tic.function_space(), name="Upper Bound Temperature")
# Assign the bounds
T_lb.assign(0.0)
T_ub.assign(1.0)
# Define the minimisation problem, with the goal to minimise the reduced functional
# Note: in some scenarios, the goal might be to maximise (rather than minimise) the functional.
minimisation_problem = MinimizationProblem(reduced_functional, bounds=(T_lb, T_ub))
Using the Lin-Moré optimiser¶
In this tutorial, we employ the trust region method of Lin and Moré (1999) implemented in ROL (Rapid Optimization Library). Lin-Moré is a truncated Newton method, which involves the repeated application of an iterative algorithm to approximately solve Newton’s equations (Dembo and Steihaug, 1983).
Lin-Moré effectively handles provided bound constraints by ensuring that variables remain within their specified bounds. During each iteration, variables are classified into "active" and "inactive" sets. Variables at their bounds that do not allow descent are considered active and are fixed during the iteration. The remaining variables, which can change without violating the bounds, are inactive. These properties make the algorithm robust and efficient for solving bound-constrained optimisation problems.
For our solution of the optimisation problem we use the pre-defined paramters set in gadopt by using minimsation_parameters.
Here, we set the number of iterations to only 5, as opposed to the default 100. We also adjust the step-length for this problem,
by setting it to a lower value than our default.
minimisation_parameters["Status Test"]["Iteration Limit"] = 5
minimisation_parameters["Step"]["Trust Region"]["Initial Radius"] = 1e-2
A notable feature of this optimisation approach in ROL is its checkpointing capability. For every iteration,
all information necessary to restart the optimisation from that iteration is saved in the specified checkpoint_dir.
# Define the LinMore Optimiser class with checkpointing capability:
optimiser = LinMoreOptimiser(
minimisation_problem,
minimisation_parameters,
checkpoint_dir="optimisation_checkpoint",
)
For sake of book-keeping the simulation, we have also implemented a user-defined way of
recording information that might be used to check the optimisation performance. This
callback function will be executed at the end of each iteration. Here, we write out
the control field, i.e., the reconstructed intial temperature field, at the end of
each iteration. To access the last value of an overloaded object we should access the
.block_variable.checkpoint method as below.
For the sake of this demo, we also record the values of the reduced functional directly in order to produce a plot of the convergence.
solutions_vtk = VTKFile("solutions.pvd")
solution_container = Function(Tic.function_space(), name="Solutions")
functional_values = []
def callback():
solution_container.assign(Tic.block_variable.checkpoint)
solutions_vtk.write(solution_container)
final_temperature_misfit = assemble(
(T.block_variable.checkpoint - Tobs) ** 2 * dx
)
log(f"Terminal Temperature Misfit: {final_temperature_misfit}")
def record_value(value, *args):
functional_values.append(value)
optimiser.add_callback(callback)
reduced_functional.eval_cb_post = record_value
# If it existed, we could restore the optimisation from last checkpoint:
# optimiser.restore()
# Run the optimisation
optimiser.run()
# Write the functional values to a file
with open("functional.txt", "w") as f:
f.write("\n".join(str(x) for x in functional_values))
Lin-More Trust-Region Method (Type B, Bound Constraints) iter value gnorm snorm delta #fval #grad #hess #proj tr_flag iterCG flagCG 0 4.357895e-02 4.000518e-01 --- 1.000000e-02 1 1 0 2 --- --- ---
Terminal Temperature Misfit: 0.04066408291036511
1 3.781383e-02 3.809798e-01 1.000000e-02 1.000000e-01 2 2 3 7 0 1 3
Terminal Temperature Misfit: 0.035329227197322496
2 3.484881e-03 1.247252e-01 1.000000e-01 1.000000e+00 3 3 25 22 0 10 1
Terminal Temperature Misfit: 0.0033231979046779
3 1.052985e-03 1.764330e-01 3.867166e-02 1.000000e+00 4 4 30 27 0 2 0
Terminal Temperature Misfit: 0.0005034484967424784
4 1.052985e-03 1.764330e-01 2.335888e-02 5.839719e-03 5 4 42 31 2 8 0
Terminal Temperature Misfit: 0.0005034484967424784
5 5.887252e-04 7.979011e-02 5.839719e-03 5.839719e-03 6 5 63 45 0 10 1
Terminal Temperature Misfit: 0.0004445672032201521 Optimization Terminated with Status: Last Type (Dummy)
At this point a total number of 5 iterations are performed. For the example
case here with 10 timesteps this should result an adequete reduction
in the objective functional. Now we can look at the solution
visually. For the actual simulation with 80 time-steps, this solution
could be compared to Tic_ref as the "true solution".
import pyvista as pv
VTKFile("./solution.pvd").write(optimiser.rol_solver.rolvector.dat[0])
dataset = pv.read('./solution.pvd')
# Create a plotter object
plotter = pv.Plotter()
# Add the dataset to the plotter
plotter.add_mesh(dataset, scalars=dataset[0].array_names[0], cmap='coolwarm')
plotter.add_text("Solution after 5 iterations", font_size=10)
# Adjust the camera position
plotter.camera_position = [(0.5, 0.5, 2.5), (0.5, 0.5, 0), (0, 1, 0)]
# Show the plot
plotter.show(jupyter_backend="static")
import matplotlib.pyplot as plt
plt.plot(functional_values)
plt.xlabel("Optimisation iteration")
plt.ylabel("Reduced functional")
plt.title("Optimisation convergence")
Text(0.5, 1.0, 'Optimisation convergence')
