Merge remote-tracking branch 'upstream/master'

Author: tlunet

pySDC/implementations/hooks/log_errors.py

@@ -0,0 +1,116 @@
+import numpy as np
+from pySDC.core.Hooks import hooks
+
+
+class LogGlobalError(hooks):
+    """
+    Log the global error with respect to `u_exact` defined in the problem class as "e_global".
+    Be aware that this requires the problems to be compatible with this. We need some kind of "exact" solution for this
+    to work, be it a reference solution or something analytical.
+    """
+
+    def post_step(self, step, level_number):
+
+        super(LogGlobalError, self).post_step(step, level_number)
+
+        # some abbreviations
+        L = step.levels[level_number]
+
+        L.sweep.compute_end_point()
+
+        self.add_to_stats(
+            process=step.status.slot,
+            time=L.time + L.dt,
+            level=L.level_index,
+            iter=step.status.iter,
+            sweep=L.status.sweep,
+            type='e_global',
+            value=abs(L.prob.u_exact(t=L.time + L.dt) - L.uend),
+        )
+
+
+class LogGlobalErrorPostRun(hooks):
+    """
+    Compute the global error once after the run is finished.
+    """
+
+    def __init__(self):
+        """
+        Add an attribute for when the last solution was added.
+        """
+        super().__init__()
+        self.__t_last_solution = 0
+
+    def post_step(self, step, level_number):
+        """
+        Store the time at which the solution is stored.
+        This is required because between the `post_step` hook where the solution is stored and the `post_run` hook
+        where the error is stored, the step size can change.
+
+        Args:
+            step (pySDC.Step.step): The current step
+            level_number (int): The index of the level
+
+        Returns:
+            None
+        """
+        super().post_step(step, level_number)
+        self.__t_last_solution = step.levels[0].time + step.levels[0].dt
+
+    def post_run(self, step, level_number):
+        """
+        Log the global error.
+
+        Args:
+            step (pySDC.Step.step): The current step
+            level_number (int): The index of the level
+
+        Returns:
+            None
+        """
+        super().post_run(step, level_number)
+
+        if level_number == 0:
+            L = step.levels[level_number]
+
+            e_glob = np.linalg.norm(L.prob.u_exact(t=self.__t_last_solution) - L.uend, np.inf)
+
+            if step.status.last:
+                self.logger.info(f'Finished with a global error of e={e_glob:.2e}')
+
+            self.add_to_stats(
+                process=step.status.slot,
+                time=L.time + L.dt,
+                level=L.level_index,
+                iter=step.status.iter,
+                sweep=L.status.sweep,
+                type='e_global',
+                value=e_glob,
+            )
+
+
+class LogLocalError(hooks):
+    """
+    Log the local error with respect to `u_exact` defined in the problem class as "e_local".
+    Be aware that this requires the problems to be compatible with this. In particular, a reference solution needs to
+    be made available from the initial conditions of the step, not of the run. Otherwise you compute the global error.
+    """
+
+    def post_step(self, step, level_number):
+
+        super(LogLocalError, self).post_step(step, level_number)
+
+        # some abbreviations
+        L = step.levels[level_number]
+
+        L.sweep.compute_end_point()
+
+        self.add_to_stats(
+            process=step.status.slot,
+            time=L.time + L.dt,
+            level=L.level_index,
+            iter=step.status.iter,
+            sweep=L.status.sweep,
+            type='e_local',
+            value=abs(L.prob.u_exact(t=L.time + L.dt, u_init=L.u[0], t_init=L.time) - L.uend),
+        )

pySDC/implementations/hooks/log_solution.py

@@ -31,3 +31,35 @@ def post_step(self, step, level_number):
             type='u',
             value=L.uend,
         )
+
+
+class LogSolutionAfterIteration(hooks):
+    """
+    Store the solution at the end of each iteration as "u".
+    """
+
+    def post_iteration(self, step, level_number):
+        """
+        Record solution at the end of the iteration
+
+        Args:
+            step (pySDC.Step.step): the current step
+            level_number (int): the current level number
+
+        Returns:
+            None
+        """
+        super().post_iteration(step, level_number)
+
+        L = step.levels[level_number]
+        L.sweep.compute_end_point()
+
+        self.add_to_stats(
+            process=step.status.slot,
+            time=L.time + L.dt,
+            level=L.level_index,
+            iter=step.status.iter,
+            sweep=L.status.sweep,
+            type='u',
+            value=L.uend,
+        )

pySDC/implementations/problem_classes/Lorenz.py

@@ -0,0 +1,166 @@
+import numpy as np
+from pySDC.core.Problem import ptype
+from pySDC.implementations.datatype_classes.mesh import mesh
+
+
+class LorenzAttractor(ptype):
+    """
+    Simple script to run a Lorenz attractor problem.
+
+    The Lorenz attractor is a system of three ordinary differential equations that exhibits some chaotic behaviour.
+    It is well known for the "Butterfly Effect", because the solution looks like a butterfly (solve to Tend = 100 or
+    so to see this with these initial conditions) and because of the chaotic nature.
+
+    Since the problem is non-linear, we need to use a Newton solver.
+
+    Problem and initial conditions do not originate from, but were taken from doi.org/10.2140/camcos.2015.10.1
+    """
+
+    def __init__(self, problem_params):
+        """
+        Initialization routine
+
+        Args:
+            problem_params (dict): custom parameters for the example
+        """
+
+        # take care of essential parameters in defaults such that they always exist
+        defaults = {
+            'sigma': 10.0,
+            'rho': 28.0,
+            'beta': 8.0 / 3.0,
+            'nvars': 3,
+            'newton_tol': 1e-9,
+            'newton_maxiter': 99,
+        }
+
+        for key in defaults.keys():
+            problem_params[key] = problem_params.get(key, defaults[key])
+
+        # invoke super init, passing number of dofs, dtype_u and dtype_f
+        super().__init__(
+            init=(problem_params['nvars'], None, np.dtype('float64')),
+            dtype_u=mesh,
+            dtype_f=mesh,
+            params=problem_params,
+        )
+
+    def eval_f(self, u, t):
+        """
+        Routine to evaluate the RHS
+
+        Args:
+            u (dtype_u): current values
+            t (float): current time
+
+        Returns:
+            dtype_f: the RHS
+        """
+        # abbreviations
+        sigma = self.params.sigma
+        rho = self.params.rho
+        beta = self.params.beta
+
+        f = self.dtype_f(self.init)
+
+        f[0] = sigma * (u[1] - u[0])
+        f[1] = rho * u[0] - u[1] - u[0] * u[2]
+        f[2] = u[0] * u[1] - beta * u[2]
+        return f
+
+    def solve_system(self, rhs, dt, u0, t):
+        """
+        Simple Newton solver for the nonlinear system.
+        Notice that I did not go through the trouble of inverting the Jacobian beforehand. If you have some time on your
+        hands feel free to do that! In the current implementation it is inverted using `numpy.linalg.solve`, which is a
+        bit more expensive than simple matrix-vector multiplication.
+
+        Args:
+            rhs (dtype_f): right-hand side for the linear system
+            dt (float): abbrev. for the local stepsize (or any other factor required)
+            u0 (dtype_u): initial guess for the iterative solver
+            t (float): current time (e.g. for time-dependent BCs)
+
+        Returns:
+            dtype_u: solution as mesh
+        """
+
+        # abbreviations
+        sigma = self.params.sigma
+        rho = self.params.rho
+        beta = self.params.beta
+
+        # start Newton iterations
+        u = self.dtype_u(u0)
+        res = np.inf
+        for _n in range(0, self.params.newton_maxiter):
+
+            # assemble G such that G(u) = 0 at the solution to the step
+            G = np.array(
+                [
+                    u[0] - dt * sigma * (u[1] - u[0]) - rhs[0],
+                    u[1] - dt * (rho * u[0] - u[1] - u[0] * u[2]) - rhs[1],
+                    u[2] - dt * (u[0] * u[1] - beta * u[2]) - rhs[2],
+                ]
+            )
+
+            # compute the residual and determine if we are done
+            res = np.linalg.norm(G, np.inf)
+            if res <= self.params.newton_tol or np.isnan(res):
+                break
+
+            # assemble Jacobian J of G
+            J = np.array(
+                [
+                    [1.0 + dt * sigma, -dt * sigma, 0],
+                    [-dt * (rho - u[2]), 1 + dt, dt * u[0]],
+                    [-dt * u[1], -dt * u[0], 1.0 + dt * beta],
+                ]
+            )
+
+            # solve the linear system for the Newton correction J delta = G
+            delta = np.linalg.solve(J, G)
+
+            # update solution
+            u = u - delta
+
+        return u
+
+    def u_exact(self, t, u_init=None, t_init=None):
+        """
+        Routine to return initial conditions or to approximate exact solution using scipy.
+
+        Args:
+            t (float): current time
+            u_init (pySDC.implementations.problem_classes.Lorenz.dtype_u): initial conditions for getting the exact solution
+            t_init (float): the starting time
+
+        Returns:
+            dtype_u: exact solution
+        """
+        me = self.dtype_u(self.init)
+
+        if t > 0:
+            from scipy.integrate import solve_ivp
+
+            def rhs(t, u):
+                """
+                Evaluate the right hand side, but switch the arguments for scipy.
+
+                Args:
+                    t (float): Time
+                    u (numpy.ndarray): Solution at time t
+
+                Returns:
+                    (numpy.ndarray): Right hand side evaluation
+                """
+                return self.eval_f(u, t)
+
+            tol = 100 * np.finfo(float).eps
+            u_init = self.u_exact(t=0) if u_init is None else u_init
+            t_init = 0 if t_init is None else t_init
+
+            me[:] = solve_ivp(rhs, (t_init, t), u_init, rtol=tol, atol=tol).y[:, -1]
+        else:
+            me[:] = 1.0
+        return me