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Python

# Authors: Nils Wagner, Ed Schofield, Pauli Virtanen, John Travers
"""
Tests for numerical integration.
"""
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy import (arange, zeros, array, dot, sqrt, cos, sin, eye, pi, exp,
allclose)
from scipy._lib._numpy_compat import _assert_warns
from scipy._lib.six import xrange
from numpy.testing import (
assert_, assert_array_almost_equal,
assert_allclose, assert_array_equal, assert_equal)
from pytest import raises as assert_raises
from scipy.integrate import odeint, ode, complex_ode
#------------------------------------------------------------------------------
# Test ODE integrators
#------------------------------------------------------------------------------
class TestOdeint(object):
# Check integrate.odeint
def _do_problem(self, problem):
t = arange(0.0, problem.stop_t, 0.05)
# Basic case
z, infodict = odeint(problem.f, problem.z0, t, full_output=True)
assert_(problem.verify(z, t))
# Use tfirst=True
z, infodict = odeint(lambda t, y: problem.f(y, t), problem.z0, t,
full_output=True, tfirst=True)
assert_(problem.verify(z, t))
if hasattr(problem, 'jac'):
# Use Dfun
z, infodict = odeint(problem.f, problem.z0, t, Dfun=problem.jac,
full_output=True)
assert_(problem.verify(z, t))
# Use Dfun and tfirst=True
z, infodict = odeint(lambda t, y: problem.f(y, t), problem.z0, t,
Dfun=lambda t, y: problem.jac(y, t),
full_output=True, tfirst=True)
assert_(problem.verify(z, t))
def test_odeint(self):
for problem_cls in PROBLEMS:
problem = problem_cls()
if problem.cmplx:
continue
self._do_problem(problem)
class TestODEClass(object):
ode_class = None # Set in subclass.
def _do_problem(self, problem, integrator, method='adams'):
# ode has callback arguments in different order than odeint
f = lambda t, z: problem.f(z, t)
jac = None
if hasattr(problem, 'jac'):
jac = lambda t, z: problem.jac(z, t)
integrator_params = {}
if problem.lband is not None or problem.uband is not None:
integrator_params['uband'] = problem.uband
integrator_params['lband'] = problem.lband
ig = self.ode_class(f, jac)
ig.set_integrator(integrator,
atol=problem.atol/10,
rtol=problem.rtol/10,
method=method,
**integrator_params)
ig.set_initial_value(problem.z0, t=0.0)
z = ig.integrate(problem.stop_t)
assert_array_equal(z, ig.y)
assert_(ig.successful(), (problem, method))
assert_(ig.get_return_code() > 0, (problem, method))
assert_(problem.verify(array([z]), problem.stop_t), (problem, method))
class TestOde(TestODEClass):
ode_class = ode
def test_vode(self):
# Check the vode solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if problem.cmplx:
continue
if not problem.stiff:
self._do_problem(problem, 'vode', 'adams')
self._do_problem(problem, 'vode', 'bdf')
def test_zvode(self):
# Check the zvode solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if not problem.stiff:
self._do_problem(problem, 'zvode', 'adams')
self._do_problem(problem, 'zvode', 'bdf')
def test_lsoda(self):
# Check the lsoda solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if problem.cmplx:
continue
self._do_problem(problem, 'lsoda')
def test_dopri5(self):
# Check the dopri5 solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if problem.cmplx:
continue
if problem.stiff:
continue
if hasattr(problem, 'jac'):
continue
self._do_problem(problem, 'dopri5')
def test_dop853(self):
# Check the dop853 solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if problem.cmplx:
continue
if problem.stiff:
continue
if hasattr(problem, 'jac'):
continue
self._do_problem(problem, 'dop853')
def test_concurrent_fail(self):
for sol in ('vode', 'zvode', 'lsoda'):
f = lambda t, y: 1.0
r = ode(f).set_integrator(sol)
r.set_initial_value(0, 0)
r2 = ode(f).set_integrator(sol)
r2.set_initial_value(0, 0)
r.integrate(r.t + 0.1)
r2.integrate(r2.t + 0.1)
assert_raises(RuntimeError, r.integrate, r.t + 0.1)
def test_concurrent_ok(self):
f = lambda t, y: 1.0
for k in xrange(3):
for sol in ('vode', 'zvode', 'lsoda', 'dopri5', 'dop853'):
r = ode(f).set_integrator(sol)
r.set_initial_value(0, 0)
r2 = ode(f).set_integrator(sol)
r2.set_initial_value(0, 0)
r.integrate(r.t + 0.1)
r2.integrate(r2.t + 0.1)
r2.integrate(r2.t + 0.1)
assert_allclose(r.y, 0.1)
assert_allclose(r2.y, 0.2)
for sol in ('dopri5', 'dop853'):
r = ode(f).set_integrator(sol)
r.set_initial_value(0, 0)
r2 = ode(f).set_integrator(sol)
r2.set_initial_value(0, 0)
r.integrate(r.t + 0.1)
r.integrate(r.t + 0.1)
r2.integrate(r2.t + 0.1)
r.integrate(r.t + 0.1)
r2.integrate(r2.t + 0.1)
assert_allclose(r.y, 0.3)
assert_allclose(r2.y, 0.2)
class TestComplexOde(TestODEClass):
ode_class = complex_ode
def test_vode(self):
# Check the vode solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if not problem.stiff:
self._do_problem(problem, 'vode', 'adams')
else:
self._do_problem(problem, 'vode', 'bdf')
def test_lsoda(self):
# Check the lsoda solver
for problem_cls in PROBLEMS:
problem = problem_cls()
self._do_problem(problem, 'lsoda')
def test_dopri5(self):
# Check the dopri5 solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if problem.stiff:
continue
if hasattr(problem, 'jac'):
continue
self._do_problem(problem, 'dopri5')
def test_dop853(self):
# Check the dop853 solver
for problem_cls in PROBLEMS:
problem = problem_cls()
if problem.stiff:
continue
if hasattr(problem, 'jac'):
continue
self._do_problem(problem, 'dop853')
class TestSolout(object):
# Check integrate.ode correctly handles solout for dopri5 and dop853
def _run_solout_test(self, integrator):
# Check correct usage of solout
ts = []
ys = []
t0 = 0.0
tend = 10.0
y0 = [1.0, 2.0]
def solout(t, y):
ts.append(t)
ys.append(y.copy())
def rhs(t, y):
return [y[0] + y[1], -y[1]**2]
ig = ode(rhs).set_integrator(integrator)
ig.set_solout(solout)
ig.set_initial_value(y0, t0)
ret = ig.integrate(tend)
assert_array_equal(ys[0], y0)
assert_array_equal(ys[-1], ret)
assert_equal(ts[0], t0)
assert_equal(ts[-1], tend)
def test_solout(self):
for integrator in ('dopri5', 'dop853'):
self._run_solout_test(integrator)
def _run_solout_after_initial_test(self, integrator):
# Check if solout works even if it is set after the initial value.
ts = []
ys = []
t0 = 0.0
tend = 10.0
y0 = [1.0, 2.0]
def solout(t, y):
ts.append(t)
ys.append(y.copy())
def rhs(t, y):
return [y[0] + y[1], -y[1]**2]
ig = ode(rhs).set_integrator(integrator)
ig.set_initial_value(y0, t0)
ig.set_solout(solout)
ret = ig.integrate(tend)
assert_array_equal(ys[0], y0)
assert_array_equal(ys[-1], ret)
assert_equal(ts[0], t0)
assert_equal(ts[-1], tend)
def test_solout_after_initial(self):
for integrator in ('dopri5', 'dop853'):
self._run_solout_after_initial_test(integrator)
def _run_solout_break_test(self, integrator):
# Check correct usage of stopping via solout
ts = []
ys = []
t0 = 0.0
tend = 10.0
y0 = [1.0, 2.0]
def solout(t, y):
ts.append(t)
ys.append(y.copy())
if t > tend/2.0:
return -1
def rhs(t, y):
return [y[0] + y[1], -y[1]**2]
ig = ode(rhs).set_integrator(integrator)
ig.set_solout(solout)
ig.set_initial_value(y0, t0)
ret = ig.integrate(tend)
assert_array_equal(ys[0], y0)
assert_array_equal(ys[-1], ret)
assert_equal(ts[0], t0)
assert_(ts[-1] > tend/2.0)
assert_(ts[-1] < tend)
def test_solout_break(self):
for integrator in ('dopri5', 'dop853'):
self._run_solout_break_test(integrator)
class TestComplexSolout(object):
# Check integrate.ode correctly handles solout for dopri5 and dop853
def _run_solout_test(self, integrator):
# Check correct usage of solout
ts = []
ys = []
t0 = 0.0
tend = 20.0
y0 = [0.0]
def solout(t, y):
ts.append(t)
ys.append(y.copy())
def rhs(t, y):
return [1.0/(t - 10.0 - 1j)]
ig = complex_ode(rhs).set_integrator(integrator)
ig.set_solout(solout)
ig.set_initial_value(y0, t0)
ret = ig.integrate(tend)
assert_array_equal(ys[0], y0)
assert_array_equal(ys[-1], ret)
assert_equal(ts[0], t0)
assert_equal(ts[-1], tend)
def test_solout(self):
for integrator in ('dopri5', 'dop853'):
self._run_solout_test(integrator)
def _run_solout_break_test(self, integrator):
# Check correct usage of stopping via solout
ts = []
ys = []
t0 = 0.0
tend = 20.0
y0 = [0.0]
def solout(t, y):
ts.append(t)
ys.append(y.copy())
if t > tend/2.0:
return -1
def rhs(t, y):
return [1.0/(t - 10.0 - 1j)]
ig = complex_ode(rhs).set_integrator(integrator)
ig.set_solout(solout)
ig.set_initial_value(y0, t0)
ret = ig.integrate(tend)
assert_array_equal(ys[0], y0)
assert_array_equal(ys[-1], ret)
assert_equal(ts[0], t0)
assert_(ts[-1] > tend/2.0)
assert_(ts[-1] < tend)
def test_solout_break(self):
for integrator in ('dopri5', 'dop853'):
self._run_solout_break_test(integrator)
#------------------------------------------------------------------------------
# Test problems
#------------------------------------------------------------------------------
class ODE:
"""
ODE problem
"""
stiff = False
cmplx = False
stop_t = 1
z0 = []
lband = None
uband = None
atol = 1e-6
rtol = 1e-5
class SimpleOscillator(ODE):
r"""
Free vibration of a simple oscillator::
m \ddot{u} + k u = 0, u(0) = u_0 \dot{u}(0) \dot{u}_0
Solution::
u(t) = u_0*cos(sqrt(k/m)*t)+\dot{u}_0*sin(sqrt(k/m)*t)/sqrt(k/m)
"""
stop_t = 1 + 0.09
z0 = array([1.0, 0.1], float)
k = 4.0
m = 1.0
def f(self, z, t):
tmp = zeros((2, 2), float)
tmp[0, 1] = 1.0
tmp[1, 0] = -self.k / self.m
return dot(tmp, z)
def verify(self, zs, t):
omega = sqrt(self.k / self.m)
u = self.z0[0]*cos(omega*t) + self.z0[1]*sin(omega*t)/omega
return allclose(u, zs[:, 0], atol=self.atol, rtol=self.rtol)
class ComplexExp(ODE):
r"""The equation :lm:`\dot u = i u`"""
stop_t = 1.23*pi
z0 = exp([1j, 2j, 3j, 4j, 5j])
cmplx = True
def f(self, z, t):
return 1j*z
def jac(self, z, t):
return 1j*eye(5)
def verify(self, zs, t):
u = self.z0 * exp(1j*t)
return allclose(u, zs, atol=self.atol, rtol=self.rtol)
class Pi(ODE):
r"""Integrate 1/(t + 1j) from t=-10 to t=10"""
stop_t = 20
z0 = [0]
cmplx = True
def f(self, z, t):
return array([1./(t - 10 + 1j)])
def verify(self, zs, t):
u = -2j * np.arctan(10)
return allclose(u, zs[-1, :], atol=self.atol, rtol=self.rtol)
class CoupledDecay(ODE):
r"""
3 coupled decays suited for banded treatment
(banded mode makes it necessary when N>>3)
"""
stiff = True
stop_t = 0.5
z0 = [5.0, 7.0, 13.0]
lband = 1
uband = 0
lmbd = [0.17, 0.23, 0.29] # fictitious decay constants
def f(self, z, t):
lmbd = self.lmbd
return np.array([-lmbd[0]*z[0],
-lmbd[1]*z[1] + lmbd[0]*z[0],
-lmbd[2]*z[2] + lmbd[1]*z[1]])
def jac(self, z, t):
# The full Jacobian is
#
# [-lmbd[0] 0 0 ]
# [ lmbd[0] -lmbd[1] 0 ]
# [ 0 lmbd[1] -lmbd[2]]
#
# The lower and upper bandwidths are lband=1 and uband=0, resp.
# The representation of this array in packed format is
#
# [-lmbd[0] -lmbd[1] -lmbd[2]]
# [ lmbd[0] lmbd[1] 0 ]
lmbd = self.lmbd
j = np.zeros((self.lband + self.uband + 1, 3), order='F')
def set_j(ri, ci, val):
j[self.uband + ri - ci, ci] = val
set_j(0, 0, -lmbd[0])
set_j(1, 0, lmbd[0])
set_j(1, 1, -lmbd[1])
set_j(2, 1, lmbd[1])
set_j(2, 2, -lmbd[2])
return j
def verify(self, zs, t):
# Formulae derived by hand
lmbd = np.array(self.lmbd)
d10 = lmbd[1] - lmbd[0]
d21 = lmbd[2] - lmbd[1]
d20 = lmbd[2] - lmbd[0]
e0 = np.exp(-lmbd[0] * t)
e1 = np.exp(-lmbd[1] * t)
e2 = np.exp(-lmbd[2] * t)
u = np.vstack((
self.z0[0] * e0,
self.z0[1] * e1 + self.z0[0] * lmbd[0] / d10 * (e0 - e1),
self.z0[2] * e2 + self.z0[1] * lmbd[1] / d21 * (e1 - e2) +
lmbd[1] * lmbd[0] * self.z0[0] / d10 *
(1 / d20 * (e0 - e2) - 1 / d21 * (e1 - e2)))).transpose()
return allclose(u, zs, atol=self.atol, rtol=self.rtol)
PROBLEMS = [SimpleOscillator, ComplexExp, Pi, CoupledDecay]
#------------------------------------------------------------------------------
def f(t, x):
dxdt = [x[1], -x[0]]
return dxdt
def jac(t, x):
j = array([[0.0, 1.0],
[-1.0, 0.0]])
return j
def f1(t, x, omega):
dxdt = [omega*x[1], -omega*x[0]]
return dxdt
def jac1(t, x, omega):
j = array([[0.0, omega],
[-omega, 0.0]])
return j
def f2(t, x, omega1, omega2):
dxdt = [omega1*x[1], -omega2*x[0]]
return dxdt
def jac2(t, x, omega1, omega2):
j = array([[0.0, omega1],
[-omega2, 0.0]])
return j
def fv(t, x, omega):
dxdt = [omega[0]*x[1], -omega[1]*x[0]]
return dxdt
def jacv(t, x, omega):
j = array([[0.0, omega[0]],
[-omega[1], 0.0]])
return j
class ODECheckParameterUse(object):
"""Call an ode-class solver with several cases of parameter use."""
# solver_name must be set before tests can be run with this class.
# Set these in subclasses.
solver_name = ''
solver_uses_jac = False
def _get_solver(self, f, jac):
solver = ode(f, jac)
if self.solver_uses_jac:
solver.set_integrator(self.solver_name, atol=1e-9, rtol=1e-7,
with_jacobian=self.solver_uses_jac)
else:
# XXX Shouldn't set_integrator *always* accept the keyword arg
# 'with_jacobian', and perhaps raise an exception if it is set
# to True if the solver can't actually use it?
solver.set_integrator(self.solver_name, atol=1e-9, rtol=1e-7)
return solver
def _check_solver(self, solver):
ic = [1.0, 0.0]
solver.set_initial_value(ic, 0.0)
solver.integrate(pi)
assert_array_almost_equal(solver.y, [-1.0, 0.0])
def test_no_params(self):
solver = self._get_solver(f, jac)
self._check_solver(solver)
def test_one_scalar_param(self):
solver = self._get_solver(f1, jac1)
omega = 1.0
solver.set_f_params(omega)
if self.solver_uses_jac:
solver.set_jac_params(omega)
self._check_solver(solver)
def test_two_scalar_params(self):
solver = self._get_solver(f2, jac2)
omega1 = 1.0
omega2 = 1.0
solver.set_f_params(omega1, omega2)
if self.solver_uses_jac:
solver.set_jac_params(omega1, omega2)
self._check_solver(solver)
def test_vector_param(self):
solver = self._get_solver(fv, jacv)
omega = [1.0, 1.0]
solver.set_f_params(omega)
if self.solver_uses_jac:
solver.set_jac_params(omega)
self._check_solver(solver)
def test_warns_on_failure(self):
# Set nsteps small to ensure failure
solver = self._get_solver(f, jac)
solver.set_integrator(self.solver_name, nsteps=1)
ic = [1.0, 0.0]
solver.set_initial_value(ic, 0.0)
_assert_warns(UserWarning, solver.integrate, pi)
class TestDOPRI5CheckParameterUse(ODECheckParameterUse):
solver_name = 'dopri5'
solver_uses_jac = False
class TestDOP853CheckParameterUse(ODECheckParameterUse):
solver_name = 'dop853'
solver_uses_jac = False
class TestVODECheckParameterUse(ODECheckParameterUse):
solver_name = 'vode'
solver_uses_jac = True
class TestZVODECheckParameterUse(ODECheckParameterUse):
solver_name = 'zvode'
solver_uses_jac = True
class TestLSODACheckParameterUse(ODECheckParameterUse):
solver_name = 'lsoda'
solver_uses_jac = True
def test_odeint_trivial_time():
# Test that odeint succeeds when given a single time point
# and full_output=True. This is a regression test for gh-4282.
y0 = 1
t = [0]
y, info = odeint(lambda y, t: -y, y0, t, full_output=True)
assert_array_equal(y, np.array([[y0]]))
def test_odeint_banded_jacobian():
# Test the use of the `Dfun`, `ml` and `mu` options of odeint.
def func(y, t, c):
return c.dot(y)
def jac(y, t, c):
return c
def jac_transpose(y, t, c):
return c.T.copy(order='C')
def bjac_rows(y, t, c):
jac = np.row_stack((np.r_[0, np.diag(c, 1)],
np.diag(c),
np.r_[np.diag(c, -1), 0],
np.r_[np.diag(c, -2), 0, 0]))
return jac
def bjac_cols(y, t, c):
return bjac_rows(y, t, c).T.copy(order='C')
c = array([[-205, 0.01, 0.00, 0.0],
[0.1, -2.50, 0.02, 0.0],
[1e-3, 0.01, -2.0, 0.01],
[0.00, 0.00, 0.1, -1.0]])
y0 = np.ones(4)
t = np.array([0, 5, 10, 100])
# Use the full Jacobian.
sol1, info1 = odeint(func, y0, t, args=(c,), full_output=True,
atol=1e-13, rtol=1e-11, mxstep=10000,
Dfun=jac)
# Use the transposed full Jacobian, with col_deriv=True.
sol2, info2 = odeint(func, y0, t, args=(c,), full_output=True,
atol=1e-13, rtol=1e-11, mxstep=10000,
Dfun=jac_transpose, col_deriv=True)
# Use the banded Jacobian.
sol3, info3 = odeint(func, y0, t, args=(c,), full_output=True,
atol=1e-13, rtol=1e-11, mxstep=10000,
Dfun=bjac_rows, ml=2, mu=1)
# Use the transposed banded Jacobian, with col_deriv=True.
sol4, info4 = odeint(func, y0, t, args=(c,), full_output=True,
atol=1e-13, rtol=1e-11, mxstep=10000,
Dfun=bjac_cols, ml=2, mu=1, col_deriv=True)
assert_allclose(sol1, sol2, err_msg="sol1 != sol2")
assert_allclose(sol1, sol3, atol=1e-12, err_msg="sol1 != sol3")
assert_allclose(sol3, sol4, err_msg="sol3 != sol4")
# Verify that the number of jacobian evaluations was the same for the
# calls of odeint with a full jacobian and with a banded jacobian. This is
# a regression test--there was a bug in the handling of banded jacobians
# that resulted in an incorrect jacobian matrix being passed to the LSODA
# code. That would cause errors or excessive jacobian evaluations.
assert_array_equal(info1['nje'], info2['nje'])
assert_array_equal(info3['nje'], info4['nje'])
# Test the use of tfirst
sol1ty, info1ty = odeint(lambda t, y, c: func(y, t, c), y0, t, args=(c,),
full_output=True, atol=1e-13, rtol=1e-11,
mxstep=10000,
Dfun=lambda t, y, c: jac(y, t, c), tfirst=True)
# The code should execute the exact same sequence of floating point
# calculations, so these should be exactly equal. We'll be safe and use
# a small tolerance.
assert_allclose(sol1, sol1ty, rtol=1e-12, err_msg="sol1 != sol1ty")
def test_odeint_errors():
def sys1d(x, t):
return -100*x
def bad1(x, t):
return 1.0/0
def bad2(x, t):
return "foo"
def bad_jac1(x, t):
return 1.0/0
def bad_jac2(x, t):
return [["foo"]]
def sys2d(x, t):
return [-100*x[0], -0.1*x[1]]
def sys2d_bad_jac(x, t):
return [[1.0/0, 0], [0, -0.1]]
assert_raises(ZeroDivisionError, odeint, bad1, 1.0, [0, 1])
assert_raises(ValueError, odeint, bad2, 1.0, [0, 1])
assert_raises(ZeroDivisionError, odeint, sys1d, 1.0, [0, 1], Dfun=bad_jac1)
assert_raises(ValueError, odeint, sys1d, 1.0, [0, 1], Dfun=bad_jac2)
assert_raises(ZeroDivisionError, odeint, sys2d, [1.0, 1.0], [0, 1],
Dfun=sys2d_bad_jac)
def test_odeint_bad_shapes():
# Tests of some errors that can occur with odeint.
def badrhs(x, t):
return [1, -1]
def sys1(x, t):
return -100*x
def badjac(x, t):
return [[0, 0, 0]]
# y0 must be at most 1-d.
bad_y0 = [[0, 0], [0, 0]]
assert_raises(ValueError, odeint, sys1, bad_y0, [0, 1])
# t must be at most 1-d.
bad_t = [[0, 1], [2, 3]]
assert_raises(ValueError, odeint, sys1, [10.0], bad_t)
# y0 is 10, but badrhs(x, t) returns [1, -1].
assert_raises(RuntimeError, odeint, badrhs, 10, [0, 1])
# shape of array returned by badjac(x, t) is not correct.
assert_raises(RuntimeError, odeint, sys1, [10, 10], [0, 1], Dfun=badjac)
def test_repeated_t_values():
"""Regression test for gh-8217."""
def func(x, t):
return -0.25*x
t = np.zeros(10)
sol = odeint(func, [1.], t)
assert_array_equal(sol, np.ones((len(t), 1)))
tau = 4*np.log(2)
t = [0]*9 + [tau, 2*tau, 2*tau, 3*tau]
sol = odeint(func, [1, 2], t, rtol=1e-12, atol=1e-12)
expected_sol = np.array([[1.0, 2.0]]*9 +
[[0.5, 1.0],
[0.25, 0.5],
[0.25, 0.5],
[0.125, 0.25]])
assert_allclose(sol, expected_sol)
# Edge case: empty t sequence.
sol = odeint(func, [1.], [])
assert_array_equal(sol, np.array([], dtype=np.float64).reshape((0, 1)))
# t values are not monotonic.
assert_raises(ValueError, odeint, func, [1.], [0, 1, 0.5, 0])
assert_raises(ValueError, odeint, func, [1, 2, 3], [0, -1, -2, 3])