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- import numpy as np
- from scipy.integrate import ode
- from .common import validate_tol, validate_first_step, warn_extraneous
- from .base import OdeSolver, DenseOutput
- class LSODA(OdeSolver):
- """Adams/BDF method with automatic stiffness detection and switching.
- This is a wrapper to the Fortran solver from ODEPACK [1]_. It switches
- automatically between the nonstiff Adams method and the stiff BDF method.
- The method was originally detailed in [2]_.
- Parameters
- ----------
- fun : callable
- Right-hand side of the system. The calling signature is ``fun(t, y)``.
- Here ``t`` is a scalar, and there are two options for the ndarray ``y``:
- It can either have shape (n,); then ``fun`` must return array_like with
- shape (n,). Alternatively it can have shape (n, k); then ``fun``
- must return an array_like with shape (n, k), i.e. each column
- corresponds to a single column in ``y``. The choice between the two
- options is determined by `vectorized` argument (see below). The
- vectorized implementation allows a faster approximation of the Jacobian
- by finite differences (required for this solver).
- t0 : float
- Initial time.
- y0 : array_like, shape (n,)
- Initial state.
- t_bound : float
- Boundary time - the integration won't continue beyond it. It also
- determines the direction of the integration.
- first_step : float or None, optional
- Initial step size. Default is ``None`` which means that the algorithm
- should choose.
- min_step : float, optional
- Minimum allowed step size. Default is 0.0, i.e., the step size is not
- bounded and determined solely by the solver.
- max_step : float, optional
- Maximum allowed step size. Default is np.inf, i.e., the step size is not
- bounded and determined solely by the solver.
- rtol, atol : float and array_like, optional
- Relative and absolute tolerances. The solver keeps the local error
- estimates less than ``atol + rtol * abs(y)``. Here `rtol` controls a
- relative accuracy (number of correct digits), while `atol` controls
- absolute accuracy (number of correct decimal places). To achieve the
- desired `rtol`, set `atol` to be smaller than the smallest value that
- can be expected from ``rtol * abs(y)`` so that `rtol` dominates the
- allowable error. If `atol` is larger than ``rtol * abs(y)`` the
- number of correct digits is not guaranteed. Conversely, to achieve the
- desired `atol` set `rtol` such that ``rtol * abs(y)`` is always smaller
- than `atol`. If components of y have different scales, it might be
- beneficial to set different `atol` values for different components by
- passing array_like with shape (n,) for `atol`. Default values are
- 1e-3 for `rtol` and 1e-6 for `atol`.
- jac : None or callable, optional
- Jacobian matrix of the right-hand side of the system with respect to
- ``y``. The Jacobian matrix has shape (n, n) and its element (i, j) is
- equal to ``d f_i / d y_j``. The function will be called as
- ``jac(t, y)``. If None (default), the Jacobian will be
- approximated by finite differences. It is generally recommended to
- provide the Jacobian rather than relying on a finite-difference
- approximation.
- lband, uband : int or None
- Parameters defining the bandwidth of the Jacobian,
- i.e., ``jac[i, j] != 0 only for i - lband <= j <= i + uband``. Setting
- these requires your jac routine to return the Jacobian in the packed format:
- the returned array must have ``n`` columns and ``uband + lband + 1``
- rows in which Jacobian diagonals are written. Specifically
- ``jac_packed[uband + i - j , j] = jac[i, j]``. The same format is used
- in `scipy.linalg.solve_banded` (check for an illustration).
- These parameters can be also used with ``jac=None`` to reduce the
- number of Jacobian elements estimated by finite differences.
- vectorized : bool, optional
- Whether `fun` is implemented in a vectorized fashion. A vectorized
- implementation offers no advantages for this solver. Default is False.
- Attributes
- ----------
- n : int
- Number of equations.
- status : string
- Current status of the solver: 'running', 'finished' or 'failed'.
- t_bound : float
- Boundary time.
- direction : float
- Integration direction: +1 or -1.
- t : float
- Current time.
- y : ndarray
- Current state.
- t_old : float
- Previous time. None if no steps were made yet.
- nfev : int
- Number of evaluations of the right-hand side.
- njev : int
- Number of evaluations of the Jacobian.
- References
- ----------
- .. [1] A. C. Hindmarsh, "ODEPACK, A Systematized Collection of ODE
- Solvers," IMACS Transactions on Scientific Computation, Vol 1.,
- pp. 55-64, 1983.
- .. [2] L. Petzold, "Automatic selection of methods for solving stiff and
- nonstiff systems of ordinary differential equations", SIAM Journal
- on Scientific and Statistical Computing, Vol. 4, No. 1, pp. 136-148,
- 1983.
- """
- def __init__(self, fun, t0, y0, t_bound, first_step=None, min_step=0.0,
- max_step=np.inf, rtol=1e-3, atol=1e-6, jac=None, lband=None,
- uband=None, vectorized=False, **extraneous):
- warn_extraneous(extraneous)
- super().__init__(fun, t0, y0, t_bound, vectorized)
- if first_step is None:
- first_step = 0 # LSODA value for automatic selection.
- else:
- first_step = validate_first_step(first_step, t0, t_bound)
- first_step *= self.direction
- if max_step == np.inf:
- max_step = 0 # LSODA value for infinity.
- elif max_step <= 0:
- raise ValueError("`max_step` must be positive.")
- if min_step < 0:
- raise ValueError("`min_step` must be nonnegative.")
- rtol, atol = validate_tol(rtol, atol, self.n)
- solver = ode(self.fun, jac)
- solver.set_integrator('lsoda', rtol=rtol, atol=atol, max_step=max_step,
- min_step=min_step, first_step=first_step,
- lband=lband, uband=uband)
- solver.set_initial_value(y0, t0)
- # Inject t_bound into rwork array as needed for itask=5.
- solver._integrator.rwork[0] = self.t_bound
- solver._integrator.call_args[4] = solver._integrator.rwork
- self._lsoda_solver = solver
- def _step_impl(self):
- solver = self._lsoda_solver
- integrator = solver._integrator
- # From lsoda.step and lsoda.integrate itask=5 means take a single
- # step and do not go past t_bound.
- itask = integrator.call_args[2]
- integrator.call_args[2] = 5
- solver._y, solver.t = integrator.run(
- solver.f, solver.jac or (lambda: None), solver._y, solver.t,
- self.t_bound, solver.f_params, solver.jac_params)
- integrator.call_args[2] = itask
- if solver.successful():
- self.t = solver.t
- self.y = solver._y
- # From LSODA Fortran source njev is equal to nlu.
- self.njev = integrator.iwork[12]
- self.nlu = integrator.iwork[12]
- return True, None
- else:
- return False, 'Unexpected istate in LSODA.'
- def _dense_output_impl(self):
- iwork = self._lsoda_solver._integrator.iwork
- rwork = self._lsoda_solver._integrator.rwork
- order = iwork[14]
- h = rwork[11]
- yh = np.reshape(rwork[20:20 + (order + 1) * self.n],
- (self.n, order + 1), order='F').copy()
- return LsodaDenseOutput(self.t_old, self.t, h, order, yh)
- class LsodaDenseOutput(DenseOutput):
- def __init__(self, t_old, t, h, order, yh):
- super().__init__(t_old, t)
- self.h = h
- self.yh = yh
- self.p = np.arange(order + 1)
- def _call_impl(self, t):
- if t.ndim == 0:
- x = ((t - self.t) / self.h) ** self.p
- else:
- x = ((t - self.t) / self.h) ** self.p[:, None]
- return np.dot(self.yh, x)
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