def test_instruction_wrong_step_factor():
f = Frame()
fi = Field(f, 0.)
with pytest.raises(TypeError):
i = Instruction(schemes.expl_1_euler, fi, fstep=None)
with pytest.raises(ValueError):
i = Instruction(schemes.expl_1_euler, fi, fstep=0.)
with pytest.raises(ValueError):
i = Instruction(schemes.expl_1_euler, fi, fstep=1.1)
def initialize(self):
'''Function initializes the simulation frame.
Function sets all fields that are None with a standard value.
If the grids are not set, it will call ``Simulation.makegrids()`` first.'''
if not isinstance(self.grid.Nm, Field) or not isinstance(self.grid.Nr, Field):
self.makegrids()
# INTEGRATION VARIABLE
if self.t is None:
self.t = IntVar(self, 0., description="Time [s]")
self.t.cfl = 0.1
self.t.updater = std.sim.dt
self.t.snapshots = np.logspace(3., 5., num=21, base=10.) * c.year
# STELLAR QUANTITIES
self._initializestar()
# GRID QUANTITIES
self._initializegrid()
# GAS QUANTITIES
self._initializegas()
# DUST QUANTITIES
self._initializedust()
# INTEGRATOR
if self.integrator is None:
instructions = [
Instruction(std.dust.impl_1_direct,
self.dust.Sigma,
controller={"rhs": self.dust._rhs
},
description="Dust: implicit 1st-order direct solver"
),
Instruction(std.gas.impl_1_direct,
self.gas.Sigma,
controller={"rhs": self.gas._rhs
},
description="Gas: implicit 1st-order direct solver"
),
]
self.integrator = Integrator(
self.t, description="Default integrator")
self.integrator.instructions = instructions
self.integrator.preparator = std.sim.prepare_implicit_dust
self.integrator.finalizer = std.sim.finalize_implicit_dust
# WRITER
if self.writer is None:
self.writer = hdf5writer()
# Updating the entire Simulation object including integrator finalization
self.integrator._finalize()
self.update()
def test_expl_2_heun_euler_adaptive():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return f.x.suggested
f.x.updater = dx
f.x.snapshots = [10.]
f.x.suggest(0.1)
f.integrator = Integrator(f.x)
f.integrator.instructions = [
Instruction(schemes.expl_2_heun_euler_adptv,
f.Y,
controller={"eps": 1.e-3})
]
f.run()
assert np.allclose(f.Y, 4.553150014598088e-05)
def test_impl_1_euler_gmres_fail():
f = Frame()
f.addfield("Y", 1.)
def jac(f, x):
return np.array([-1.])
f.Y.jacobinator = jac
f.addintegrationvariable("x", 0.)
def dx(f):
return 0.1
f.x.updater = dx
f.x.snapshots = [10.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [
Instruction(schemes.impl_1_euler_gmres,
f.Y,
controller={
"gmres_opt": {
"atol": 0.,
"tol": 1.e-18,
"maxiter": 1
}
})
]
with pytest.raises(StopIteration):
f.run()
def test_namespacewriter_simple():
f = Frame()
f.addfield("Y", 1.)
f.addgroup("A")
f.A.addfield("B", 0.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return 1.
f.x.updater = dx
f.x.snapshots = [1.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.expl_1_euler, f.Y)]
f.writer = writers.namespacewriter()
f.writer.dumping = True
f.run()
Y = f.writer.read.sequence("Y")
assert np.all(Y == [1., 0.])
x = f.writer.read.sequence("x")
assert np.all(x == [0., 1.])
data = f.writer.read.all()
assert np.all(data.Y == [1., 0.])
assert np.all(data.x == [0., 1.])
f.writer.reset()
def test_expl_5_dormand_prince_adptv():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return f.x.suggested
f.x.updater = dx
f.x.snapshots = [10.]
f.x.suggest(0.1)
f.integrator = Integrator(f.x)
f.integrator.instructions = [
Instruction(schemes.expl_5_dormand_prince_adptv,
f.Y,
controller={"eps": 1.e-2})
]
f.run()
assert np.allclose(f.Y, 1.8016162079480785e-06)
def test_expl_5_cash_karp_adptv():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return f.x.suggested
f.x.updater = dx
f.x.snapshots = [10.]
f.x.suggest(0.1)
f.integrator = Integrator(f.x)
f.integrator.instructions = [
Instruction(schemes.expl_5_cash_karp_adptv,
f.Y,
controller={"eps": 1.e-3})
]
f.run()
assert np.allclose(f.Y, 4.57114092616805e-05)
def test_expl_3_gottlieb_shu_adptv():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return f.x.suggested
f.x.updater = dx
f.x.snapshots = [10.]
f.x.suggest(0.1)
f.integrator = Integrator(f.x)
f.integrator.instructions = [
Instruction(schemes.expl_3_gottlieb_shu_adptv,
f.Y,
controller={"eps": 1.e-4})
]
f.run()
assert np.allclose(f.Y, 4.5390485375346277e-05)
def test_adaptive_update():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return f.x.suggested
f.x.updater = dx
f.x.snapshots = [10.]
f.x.suggest(100.)
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.expl_5_cash_karp_adptv, f.Y),
Instruction(schemes.update, f.Y)]
f.run()
assert f.Y == 5.34990702474703e-3
def test_simple_read_files():
f = Frame()
f.addgroup("A")
f.A.addfield("B", [0., 0.])
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return 1.
f.x.updater = dx
f.x.snapshots = [1.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.expl_1_euler, f.Y)]
f.writer = writers.hdf5writer()
f.run()
x = f.writer.read.sequence("x")
assert np.all(x == [0., 1.])
Y = f.writer.read.sequence("Y")
assert np.all(Y == [1., 0.])
B = f.writer.read.sequence("A.B")
assert np.all(B == [0., 0.])
with pytest.raises(TypeError):
f.writer.read.sequence(1)
data = f.writer.read.all()
assert np.all(data.x == [0., 1.])
assert np.all(data.Y == [1., 0.])
assert np.all(data.A.B == [0., 0.])
data0000 = f.writer.read.output(0)
assert np.all(data0000.x == 0.)
assert np.all(data0000.Y == 1.)
assert np.all(data0000.A.B == 0.)
with pytest.raises(RuntimeError):
f.writer.read.output(2)
shutil.rmtree(f.writer.datadir)
with pytest.raises(RuntimeError):
f.writer.datadir = "temp"
f.writer.read.all()
with pytest.raises(RuntimeError):
f.writer.read.sequence("x")
f.writer.datadir = "data"
def test_simple():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return 1.
f.x.updater = dx
f.x.snapshots = [1.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.expl_1_euler, f.Y)]
f.run()
assert f.Y == 0.
assert f.x.prevstepsize == 1.
def test_expl_2_heun():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return 0.1
f.x.updater = dx
f.x.snapshots = [10.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.expl_2_heun, f.Y)]
f.run()
assert np.allclose(f.Y, 4.6222977814657625e-05)
def test_expl_4_runge_kutta():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return 0.1
f.x.updater = dx
f.x.snapshots = [10.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.expl_4_runge_kutta, f.Y)]
f.run()
assert np.allclose(f.Y, 4.540034101629485e-05)
def test_expl_1_euler():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return 0.1
f.x.updater = dx
f.x.snapshots = [10.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.expl_1_euler, f.Y)]
f.run()
assert np.allclose(f.Y, 2.656139888758694e-05)
def test_impl_1_euler_gmres():
f = Frame()
f.addfield("Y", 1.)
def jac(f, x):
return np.array([-1.])
f.Y.jacobinator = jac
f.addintegrationvariable("x", 0.)
def dx(f):
return 0.1
f.x.updater = dx
f.x.snapshots = [10.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(schemes.impl_1_euler_gmres, f.Y)]
f.run()
assert np.allclose(f.Y, 7.256571590148018e-05)
def test_adaptive_fail():
f = Frame()
f.addfield("Y", 1.)
def dYdx(f, x, Y):
return -Y
f.Y.differentiator = dYdx
f.addintegrationvariable("x", 0.)
def dx(f):
return f.x.suggested
f.x.updater = dx
f.x.snapshots = [10.]
f.x.suggest(100.)
f.integrator = Integrator(f.x)
f.integrator.instructions = [Instruction(
schemes.expl_5_cash_karp_adptv, f.Y)]
f.integrator.maxit = 1
with pytest.raises(StopIteration):
f.run()
def test_impl_2_midpoint_direct():
f = Frame()
f.addfield("Y", 1.)
def jac(f, x):
return np.array([-1.])
f.Y.jacobinator = jac
f.addintegrationvariable("x", 0.)
def dx(f):
return 0.1
f.x.updater = dx
f.x.snapshots = [10.]
f.integrator = Integrator(f.x)
f.integrator.instructions = [
Instruction(schemes.impl_2_midpoint_direct, f.Y)
]
f.run()
assert np.allclose(f.Y, 4.5022605238147066e-05)
def test_instruction_no_field():
with pytest.raises(TypeError):
i = Instruction(schemes.expl_1_euler, None)
def setdustintegrator(self, scheme="explicit", method="cash-karp"):
"""Function sets the dust integrator.
Parameters
----------
scheme : string, optional, default : "explicit"
Possible values
{"explicit", "implicit"}
method : string, optional, default : "cash-karp"
Possible values for explicit integration
{"cash-karp"}
Possible values for implicit integration
{"direct", "gmres", "bicgstab}"""
if not isinstance(self.grid.Nm, Field) or not isinstance(self.grid.Nr, Field):
raise RuntimeError(
"The simulation frame has to be initialized before calling setdustimplicit().")
# Get index of dust instruction
for i, inst in enumerate(self.integrator.instructions):
if inst.Y is self.dust.Sigma:
break
if scheme == "implicit":
shape2ravel = (int(self.grid.Nr*self.grid.Nm))
# Hidden fields
# We store the old values of the surface density in a hidden field
# to calculate the fluxes through the boundaries in case of implicit integration.
self.dust._SigmaOld = Field(
self, self.dust.Sigma, description="Previous value of surface density [g/cm²]")
# The right-hand side of the matrix equation is stored in a hidden field
self.dust._rhs = Field(self, np.zeros(
shape2ravel), description="Right-hand side of matrix equation [g/cm²]")
# Setting the Jacobinator
self.dust.Sigma.jacobinator = std.dust.jacobian
# Time step routine
self.t.updater = std.sim.dt
# Updaters
self.dust.v.updater = ["frag", "driftmax", "rel"]
self.dust.updater = ["delta", "rhos", "fill", "a", "St", "H",
"rho", "backreaction", "v", "D", "eps", "kernel", "p", "S"]
self.dust.S.updater = ["ext", "tot"]
# Preparation/Finalization
self.integrator.preparator = std.sim.prepare_implicit_dust
self.integrator.finalizer = std.sim.finalize_implicit_dust
# Integrator
if method == "direct":
inst = Instruction(std.dust.impl_1_direct,
self.dust.Sigma,
controller={"rhs": self.dust._rhs
},
description="Dust: implicit 1st-order direct solver"
)
self.integrator.instructions[i] = inst
elif method == "gmres":
raise NotImplementedError(
"GMRES method is not implemented, yet.")
elif method == "bicgstab":
raise NotImplementedError("BiCGSTAB is not implemented, yet.")
else:
raise RuntimeError("Invalid method for implicit integration.")
elif scheme == "explicit":
# Remove hidden fields if they exist
if hasattr(self.dust, "_SigmaOld"):
del self.dust._SigmaOld
if hasattr(self.dust, "_rhs"):
del self.dust._rhs
# Unset Jacobian
self.dust.Sigma.jacobinator = None
# Updaters
self.dust.v.updater = ["frag", "driftmax", "rad", "rel"]
self.dust.updater = ["delta", "rhos", "fill", "a", "St", "H",
"rho", "backreaction", "v", "D", "eps", "Fi", "kernel", "p", "S"]
self.dust.S.updater = ["coag", "hyd", "ext", "tot"]
# Preparation/Finalization
self.integrator.preparator = std.sim.prepare_explicit_dust
self.integrator.finalizer = std.sim.finalize_explicit_dust
if method == "cash-karp":
# Adaptive time step routine
self.t.updater = std.sim.dt_adaptive
# Instruction
inst = Instruction(schemes.expl_5_cash_karp_adptv,
self.dust.Sigma,
controller={"dYdx": self.dust.S.tot,
"eps": 0.1,
"S": 0.9,
},
description="Dust: explicit 5th-order adaptive Cash-Karp method"
)
self.integrator.instructions[i] = inst
self.t.suggest(1.*c.year)
else:
raise RuntimeError("Invalid method for explicit integration.")
else:
raise RuntimeError("Unknown integration scheme.")
self.integrator._finalize()
self.update()
if self.verbosity > 0:
msg = "Setting dust integrator\n scheme: {}\n method: {}".format(
colorize(scheme, "blue"), colorize(method, "blue"))
print(msg)