def extract_terms(form: Form) -> SplitTimeForm:
"""Extract terms from a :class:`~ufl.Form`.
This splits a form (a sum of integrals) into those integrals which
do contain a :class:`~.TimeDerivative` and those that don't.
:arg form: The form to split.
:returns: a :class:`~.SplitTimeForm` tuple.
:raises ValueError: if the form does not apply anything other than
first-order time derivatives to a single coefficient.
"""
time_terms = []
rest_terms = []
for integral in form.integrals():
integrand = integral.integrand()
rest = remove_if(integrand, lambda o: isinstance(o, TimeDerivative))
time = remove_if(integrand, partial(contains, summands(rest)))
if not isinstance(time, Zero):
time_terms.append(integral.reconstruct(integrand=time))
if not isinstance(rest, Zero):
rest_terms.append(integral.reconstruct(integrand=rest))
time_terms = check_integrals(time_terms, expect_time_derivative=True)
rest_terms = check_integrals(rest_terms, expect_time_derivative=False)
return SplitTimeForm(time=Form(time_terms), remainder=Form(rest_terms))
def transform_integrands(form, transform, domain_type=None):
"""Apply transform(expression) to each integrand
expression in form, or to form if it is an Expr."""
if isinstance(form, Form):
newintegrals = []
for itg in form.integrals():
integrand = itg.integrand()
if domain_type is None or domain_type == itg.domain_type():
integrand = transform(integrand)
if not isinstance(integrand, Zero):
newitg = itg.reconstruct(integrand)
newintegrals.append(newitg)
if not newintegrals:
debug(
"No integrals left after transformation, returning empty form."
)
return Form(newintegrals)
elif isinstance(form, Integral):
integral = form
integrand = transform(integral.integrand())
new_integral = integral.reconstruct(integrand)
return new_integral
elif isinstance(form, Expr):
expr = form
return transform(expr)
else:
error("Expecting Form or Expr.")
def map_integrands(function, form, only_integral_type=None):
"""Apply transform(expression) to each integrand
expression in form, or to form if it is an Expr.
"""
if isinstance(form, Form):
mapped_integrals = [
map_integrands(function, itg, only_integral_type)
for itg in form.integrals()
]
nonzero_integrals = [
itg for itg in mapped_integrals
if not isinstance(itg.integrand(), Zero)
]
return Form(nonzero_integrals)
elif isinstance(form, Integral):
itg = form
if (only_integral_type is None) or (itg.integral_type()
in only_integral_type):
return itg.reconstruct(function(itg.integrand()))
else:
return itg
elif isinstance(form, Expr):
integrand = form
return function(integrand)
else:
error("Expecting Form, Integral or Expr.")
def derivative(form, coefficient, argument=None, coefficient_derivatives=None):
"""UFL form operator:
Compute the Gateaux derivative of *form* w.r.t. *coefficient* in direction
of *argument*.
If the argument is omitted, a new ``Argument`` is created
in the same space as the coefficient, with argument number
one higher than the highest one in the form.
The resulting form has one additional ``Argument``
in the same finite element space as the coefficient.
A tuple of ``Coefficient`` s may be provided in place of
a single ``Coefficient``, in which case the new ``Argument``
argument is based on a ``MixedElement`` created from this tuple.
An indexed ``Coefficient`` from a mixed space may be provided,
in which case the argument should be in the corresponding
subspace of the coefficient space.
If provided, *coefficient_derivatives* should be a mapping from
``Coefficient`` instances to their derivatives w.r.t. *coefficient*.
"""
coefficients, arguments = _handle_derivative_arguments(form, coefficient,
argument)
if coefficient_derivatives is None:
coefficient_derivatives = ExprMapping()
else:
cd = []
for k in sorted_expr(coefficient_derivatives.keys()):
cd += [as_ufl(k), as_ufl(coefficient_derivatives[k])]
coefficient_derivatives = ExprMapping(*cd)
# Got a form? Apply derivatives to the integrands in turn.
if isinstance(form, Form):
integrals = []
for itg in form.integrals():
if not isinstance(coefficient, SpatialCoordinate):
fd = CoefficientDerivative(itg.integrand(), coefficients,
arguments, coefficient_derivatives)
else:
fd = CoordinateDerivative(itg.integrand(), coefficients,
arguments, coefficient_derivatives)
integrals.append(itg.reconstruct(fd))
return Form(integrals)
elif isinstance(form, Expr):
# What we got was in fact an integrand
if not isinstance(coefficient, SpatialCoordinate):
return CoefficientDerivative(form, coefficients,
arguments, coefficient_derivatives)
else:
return CoordinateDerivative(form, coefficients,
arguments, coefficient_derivatives)
error("Invalid argument type %s." % str(type(form)))
def strip_dt_form(F):
if isinstance(F, Zero):
# Avoid applying the time derivative stripper to zero forms
return F
stripper = Memoizer(strip_dt)
# Strip dt from all the integrals in the form
Fnew = Form([
i.reconstruct(integrand=stripper(i.integrand()))
for i in F.integrals()
])
# Return the form stripped of its time derivatives
return Fnew
def group_form_integrals(form, domains):
"""Group integrals by domain and type, performing canonical simplification.
:arg form: the :class:`~.Form` to group the integrals of.
:arg domains: an iterable of :class:`~.Domain`\s.
:returns: A new :class:`~.Form` with gathered integrands.
"""
# Group integrals by domain and type
integrals_by_domain_and_type = \
group_integrals_by_domain_and_type(form.integrals(), domains)
integrals = []
for domain in domains:
for integral_type in ufl.measure.integral_types():
# Get integrals with this domain and type
ddt_integrals = integrals_by_domain_and_type.get(
(domain, integral_type))
if ddt_integrals is None:
continue
# Group integrals by subdomain id, after splitting e.g.
# f*dx((1,2)) + g*dx((2,3)) -> f*dx(1) + (f+g)*dx(2) + g*dx(3)
# (note: before this call, 'everywhere' is a valid subdomain_id,
# and after this call, 'otherwise' is a valid subdomain_id)
single_subdomain_integrals = \
rearrange_integrals_by_single_subdomains(ddt_integrals)
for subdomain_id, ss_integrals in sorted_by_key(
single_subdomain_integrals):
# Accumulate integrands of integrals that share the
# same compiler data
integrands_and_cds = \
accumulate_integrands_with_same_metadata(ss_integrals)
for integrand, metadata in integrands_and_cds:
integrals.append(
Integral(integrand, integral_type, domain,
subdomain_id, metadata, None))
return Form(integrals)
def reconstruct_form_from_integral_data(integral_data):
integrals = []
for ida in integral_data:
integrals.extend(ida.integrals)
return Form(integrals)
def group_form_integrals(form, domains, do_append_everywhere_integrals=True):
"""Group integrals by domain and type, performing canonical simplification.
:arg form: the :class:`~.Form` to group the integrals of.
:arg domains: an iterable of :class:`~.Domain`s.
:returns: A new :class:`~.Form` with gathered integrands.
"""
# Group integrals by domain and type
integrals_by_domain_and_type = \
group_integrals_by_domain_and_type(form.integrals(), domains)
integrals = []
for domain in domains:
for integral_type in ufl.measure.integral_types():
# Get integrals with this domain and type
ddt_integrals = integrals_by_domain_and_type.get(
(domain, integral_type))
if ddt_integrals is None:
continue
# Group integrals by subdomain id, after splitting e.g.
# f*dx((1,2)) + g*dx((2,3)) -> f*dx(1) + (f+g)*dx(2) + g*dx(3)
# (note: before this call, 'everywhere' is a valid subdomain_id,
# and after this call, 'otherwise' is a valid subdomain_id)
single_subdomain_integrals = \
rearrange_integrals_by_single_subdomains(ddt_integrals, do_append_everywhere_integrals)
for subdomain_id, ss_integrals in sorted_by_key(
single_subdomain_integrals):
# strip the coordinate derivatives from all integrals
# this yields a list of the form [(coordinate derivative, integral), ...]
stripped_integrals_and_coordderivs = strip_coordinate_derivatives(
ss_integrals)
# now group the integrals by the coordinate derivative
def calc_hash(cd):
return sum(
sum(tuple_elem._ufl_compute_hash_()
for tuple_elem in tuple_) for tuple_ in cd)
coordderiv_integrals_dict = {}
for integral, coordderiv in stripped_integrals_and_coordderivs:
coordderivhash = calc_hash(coordderiv)
if coordderivhash in coordderiv_integrals_dict:
coordderiv_integrals_dict[coordderivhash][1].append(
integral)
else:
coordderiv_integrals_dict[coordderivhash] = (
coordderiv, [integral])
# cd_integrals_dict is now a dict of the form
# { hash: (CoordinateDerivative, [integral, integral, ...]), ... }
# we can now put the integrals back together and then afterwards
# apply the CoordinateDerivative again
for cdhash, samecd_integrals in sorted_by_key(
coordderiv_integrals_dict):
# Accumulate integrands of integrals that share the
# same compiler data
integrands_and_cds = \
accumulate_integrands_with_same_metadata(samecd_integrals[1])
for integrand, metadata in integrands_and_cds:
integral = Integral(integrand, integral_type, domain,
subdomain_id, metadata, None)
integral = attach_coordinate_derivatives(
integral, samecd_integrals[0])
integrals.append(integral)
return Form(integrals)
def assemble(self, form, arity):
'''Assemble a biliner(2), linear(1) form'''
reduced_integrals = self.select_integrals(form) #! Selector
# Signal to xii.assemble
if not reduced_integrals: return None
components = []
for integral in form.integrals():
# Delegate to friend
if integral not in reduced_integrals:
components.append(
xii.assembler.xii_assembly.assemble(Form([integral])))
continue
reduced_mesh = integral.ufl_domain().ufl_cargo()
integrand = integral.integrand()
# Split arguments in those that need to be and those that are
# already restricted.
terminals = set(traverse_unique_terminals(integrand))
# FIXME: is it enough info (in general) to decide
terminals_to_restrict = sorted(
self.restriction_filter(terminals, reduced_mesh),
key=lambda t: self.is_compatible(t, reduced_mesh))
# You said this is a trace ingral!
assert terminals_to_restrict
# Let's pick a guy for restriction
terminal = terminals_to_restrict.pop()
# We have some assumption on the candidate
assert self.is_compatible(terminal, reduced_mesh)
data = self.reduction_matrix_data(terminal)
integrand = ufl2uflcopy(integrand)
# With sane inputs we can get the reduced element and setup the
# intermediate function space where the reduction of terminal
# lives
V = terminal.function_space()
TV = self.reduced_space(V, reduced_mesh) #! Space construc
# Setup the matrix to from space of the trace_terminal to the
# intermediate space. FIXME: normal and trace_mesh
#! mat construct
df.info('\tGetting reduction op')
rop_timer = df.Timer('rop')
T = self.reduction_matrix(V, TV, reduced_mesh, data)
df.info('\tDone (reduction op) %g' % rop_timer.stop())
# T
if is_test_function(terminal):
replacement = df.TestFunction(TV)
# Passing the args to get the comparison a make substitution
integrand = replace(integrand,
terminal,
replacement,
attributes=self.attributes)
trace_form = Form([integral.reconstruct(integrand=integrand)])
if arity == 2:
# Make attempt on the substituted form
A = xii.assembler.xii_assembly.assemble(trace_form)
components.append(block_transpose(T) * A)
else:
b = xii.assembler.xii_assembly.assemble(trace_form)
Tb = df.Function(V).vector() # Alloc and apply
T.transpmult(b, Tb)
components.append(Tb)
if is_trial_function(terminal):
assert arity == 2
replacement = df.TrialFunction(TV)
# Passing the args to get the comparison
integrand = replace(integrand,
terminal,
replacement,
attributes=self.attributes)
trace_form = Form([integral.reconstruct(integrand=integrand)])
A = xii.assembler.xii_assembly.assemble(trace_form)
components.append(A * T)
# Okay, then this guy might be a function
if isinstance(terminal, df.Function):
replacement = df.Function(TV)
# Replacement is not just a placeholder
T.mult(terminal.vector(), replacement.vector())
# Substitute
integrand = replace(integrand,
terminal,
replacement,
attributes=self.attributes)
trace_form = Form([integral.reconstruct(integrand=integrand)])
components.append(
xii.assembler.xii_assembly.assemble(trace_form))
# The whole form is then the sum of integrals
return reduce(operator.add, components)
def __rmul__(self, integrand):
"""Multiply a scalar expression with measure to construct a form with
a single integral.
This is to implement the notation
form = integrand * self
Integration properties are taken from this Measure object.
"""
# Avoid circular imports
from ufl.integral import Integral
from ufl.form import Form
# Allow python literals: 1*dx and 1.0*dx
if isinstance(integrand, (int, float)):
integrand = as_ufl(integrand)
# Let other types implement multiplication with Measure if
# they want to (to support the dolfin-adjoint TimeMeasure)
if not isinstance(integrand, Expr):
return NotImplemented
# Allow only scalar integrands
if not is_true_ufl_scalar(integrand):
error("Can only integrate scalar expressions. The integrand is a "
"tensor expression with value shape %s and free indices with labels %s." %
(integrand.ufl_shape, integrand.ufl_free_indices))
# If we have a tuple of domain ids, delegate composition to
# Integral.__add__:
subdomain_id = self.subdomain_id()
if isinstance(subdomain_id, tuple):
return sum(integrand*self.reconstruct(subdomain_id=d) for d in subdomain_id)
# Check that we have an integer subdomain or a string
# ("everywhere" or "otherwise", any more?)
if not isinstance(subdomain_id, (str, numbers.Integral,)):
error("Expecting integer or string domain id.")
# If we don't have an integration domain, try to find one in
# integrand
domain = self.ufl_domain()
if domain is None:
domains = extract_domains(integrand)
if len(domains) == 1:
domain, = domains
elif len(domains) == 0:
error("This integral is missing an integration domain.")
else:
error("Multiple domains found, making the choice of integration domain ambiguous.")
# Otherwise create and return a one-integral form
integral = Integral(integrand=integrand,
integral_type=self.integral_type(),
domain=domain,
subdomain_id=subdomain_id,
metadata=self.metadata(),
subdomain_data=self.subdomain_data())
return Form([integral])
def __rmul__(self, integrand):
# Let other types implement multiplication with Measure
# if they want to (to support the dolfin-adjoint TimeMeasure)
if not isinstance(integrand, Expr):
return NotImplemented
# Allow only scalar integrands
if not is_true_ufl_scalar(integrand):
error("Trying to integrate expression of rank %d with free indices %r." \
% (integrand.rank(), integrand.free_indices()))
# Is the measure in a state where multiplication is not allowed?
if self._domain_description == Measure.DOMAIN_ID_UNDEFINED:
error("Missing domain id. You need to select a subdomain, " +\
"e.g. M = f*dx(0) for subdomain 0.")
#else: # TODO: Do it this way instead, and move all logic below into preprocess:
# # Return a one-integral form:
# from ufl.form import Form
# return Form( [Integral(integrand, self.domain_type(), self.domain_id(), self.metadata(), self.domain_data())] )
# # or if we move domain data into Form instead:
# integrals = [Integral(integrand, self.domain_type(), self.domain_id(), self.metadata())]
# domain_data = { self.domain_type(): self.domain_data() }
# return Form(integrals, domain_data)
# TODO: How to represent all kinds of domain descriptions is still a bit unclear
# Create form if we have a sufficient domain description
elif ( # We have a complete measure with domain description
isinstance(self._domain_description, DomainDescription)
# Is the measure in a basic state 'foo*dx'?
or self._domain_description == Measure.DOMAIN_ID_UNIQUE
# Is the measure over everywhere?
or self._domain_description == Measure.DOMAIN_ID_EVERYWHERE
# Is the measure in a state not allowed prior to preprocessing?
or self._domain_description == Measure.DOMAIN_ID_OTHERWISE):
# Create and return a one-integral form
from ufl.form import Form
return Form([
Integral(integrand, self.domain_type(), self.domain_id(),
self.metadata(), self.domain_data())
])
# Did we get several ids?
elif isinstance(self._domain_description, tuple):
# FIXME: Leave this analysis to preprocessing
return sum(integrand * self.reconstruct(domain_id=d)
for d in self._domain_description)
# Did we get a name?
elif isinstance(self._domain_description, str):
# FIXME: Leave this analysis to preprocessing
# Get all domains and regions from integrand to analyse
domains = extract_domains(integrand)
# Get domain or region with this name from integrand, error if multiple found
name = self._domain_description
candidates = set()
for TD in domains:
if TD.name() == name:
candidates.add(TD)
ufl_assert(
len(candidates) > 0,
"Found no domain with name '%s' in integrand." % name)
ufl_assert(
len(candidates) == 1,
"Multiple distinct domains with same name encountered in integrand."
)
D, = candidates
# Reconstruct measure with the found named domain or region
measure = self.reconstruct(domain_id=D)
return integrand * measure
# Did we get a number?
elif isinstance(self._domain_description, int):
# FIXME: Leave this analysis to preprocessing
# Get all top level domains from integrand to analyse
domains = extract_top_domains(integrand)
# Get domain from integrand, error if multiple found
if len(domains) == 0:
# This is the partially defined integral from dolfin expression mess
cell = integrand.cell()
D = None if cell is None else as_domain(cell)
elif len(domains) == 1:
D, = domains
else:
error(
"Ambiguous reference to integer subdomain with multiple top domains in integrand."
)
if D is None:
# We have a number but not a domain? Leave it to preprocess...
# This is the case with badly formed forms which can occur from dolfin
# Create and return a one-integral form
from ufl.form import Form
return Form([
Integral(integrand, self.domain_type(), self.domain_id(),
self.metadata(), self.domain_data())
])
else:
# Reconstruct measure with the found numbered subdomain
measure = self.reconstruct(
domain_id=D[self._domain_description])
return integrand * measure
# Provide error to user
else:
error("Invalid domain id %s." % str(self._domain_description))
