def __init__(self, name, mesh, mesh_unit, region_materials,
min_region=-1):
"""
:Parameters:
`region_materials` : list of list of string
region_materials[region_nr] is a list of names (strings) of field
components (like "mat1", "mat2") available in the mesh region
with number 'region_nr'. For example, for a mesh with three
regions and region_materials=[["one", "two"], ["one", "three"],
["one"]], a field 'f' defined 'per-material' will have three
sub-fields 'f_one', 'f_two' and 'f_three' with: 'f_one' defined
everywhere, 'f_two' defined in region 0 and 'f_three' defined in
region 1.
"""
# Just save the relevant stuff
self.name = name
self.mesh = mesh
self.mesh_unit = mesh_unit
self.dim = mesh.dim
self.region_materials = region_materials
self.min_region = min_region
self.regions = \
MeshRegions(region_materials, min_region=min_region)
# Things that get constructed when the object is "used"
self.computations = Computations()
self.quantities = Quantities()
self.timesteppers = Timesteppers()
# Initialise some members
self.quantities.primary = None
self.quantities.derived = None
self.quantities.dependencies = None
self.targets = []
self.intensive_params = []
self.elems_by_field = {} # For each field: list of elems ordered
# per region
self.prototype_elems = [] # List of the prototype elements
self.sibling_elems = {}
self.mwes = {} # All the MWEs
self.lam = None
self._built = {}
class Model(object):
def __init__(self, name, mesh, mesh_unit, region_materials,
min_region=-1):
"""
:Parameters:
`region_materials` : list of list of string
region_materials[region_nr] is a list of names (strings) of field
components (like "mat1", "mat2") available in the mesh region
with number 'region_nr'. For example, for a mesh with three
regions and region_materials=[["one", "two"], ["one", "three"],
["one"]], a field 'f' defined 'per-material' will have three
sub-fields 'f_one', 'f_two' and 'f_three' with: 'f_one' defined
everywhere, 'f_two' defined in region 0 and 'f_three' defined in
region 1.
"""
# Just save the relevant stuff
self.name = name
self.mesh = mesh
self.mesh_unit = mesh_unit
self.dim = mesh.dim
self.region_materials = region_materials
self.min_region = min_region
self.regions = \
MeshRegions(region_materials, min_region=min_region)
# Things that get constructed when the object is "used"
self.computations = Computations()
self.quantities = Quantities()
self.timesteppers = Timesteppers()
# Initialise some members
self.quantities.primary = None
self.quantities.derived = None
self.quantities.dependencies = None
self.targets = []
self.intensive_params = []
self.elems_by_field = {} # For each field: list of elems ordered
# per region
self.prototype_elems = [] # List of the prototype elements
self.sibling_elems = {}
self.mwes = {} # All the MWEs
self.lam = None
self._built = {}
def _was_built(self, name):
return (name in self._built)
def add_quantity(self, *quant):
"""Add the given quantity 'quant' to the current physical model.
If 'quant' is a list, then add all the elements of the list, assuming
they all are Quantity objects."""
self.quantities.add(*quant)
_set_model(quant, self)
def add_computation(self, *c):
"""Add the computation (Computation object) to the model."""
self.computations.add(*c)
_set_model(c, self)
def add_timestepper(self, *ts):
"""Add the timestepper (Timestepper object) to the model."""
self.timesteppers.add(*ts)
_set_model(ts, self)
def _build_elems_on_material(self, name, shape):
# Build the 'elements' dictionary which maps an entity name to
# a corresponding element
elements = {}
for entity_name in self.regions.all_entity_names:
logger.info("Processing material '%s'" % entity_name)
elem_name = "%s_%s" % (name, entity_name)
elem = ocaml.make_element(elem_name, shape, self.dim, 1)
elements[entity_name] = elem
# Obtain a list fused_elem_by_region such that
# fused_elem_by_region[idx] is the element obtained by fusing all the
# elements corresponding to the materials defined in region idx.
# fused_elem_by_region[idx] is then the right element for that region
fused_elem_by_region = []
for entities_in_region in self.regions.entities_by_region:
# Build a list of the elements in the region
elems_in_region = map(elements.__getitem__, entities_in_region)
# Fuse all these elements
fused_elem = reduce(ocaml.fuse_elements, elems_in_region,
ocaml.empty_element)
fused_elem_by_region.append(fused_elem)
return fused_elem_by_region
def _build_elems_everywhere(self, name, shape):
elem = ocaml.make_element(name, shape, self.dim, 1)
return map(lambda region: elem, self.region_materials)
def _build_elems(self, name, shape, on_material=False):
shape = list(shape)
# Find whether we have built a similar field before, we may then use
# it to build the new one
for p_name, p_shape, p_elems, p_on_material in self.prototype_elems:
if p_shape == shape and p_on_material == on_material:
logger.info("Using element %s for field %s (sibling)"
% (p_name, name))
self.sibling_elems[name] = p_name
return p_elems
where = ("on material" if on_material else "everywhere")
logger.info("Building element %s %s" % (name, where))
if on_material:
elems = self._build_elems_on_material(name, shape)
else:
elems = self._build_elems_everywhere(name, shape)
self.prototype_elems.append((name, shape, elems, on_material))
self.elems_by_field[name] = elems
return elems
def _build_mwe(self, name):
if name in self.sibling_elems:
p_name = self.sibling_elems[name] # prototype name
assert not p_name in self.sibling_elems, \
"Cannot have sibling field of a sibling field."
logger.info("Building MWE %s as sibling of %s" % (name, p_name))
if p_name in self.mwes:
p_mwe = self.mwes[p_name]
else:
p_mwe = self._build_mwe(p_name)
rename_prefix = "%s/%s" % (name, p_name)
q = self.quantities._by_name[name]
if q.def_on_mat:
all_entity_names = self.regions.all_entity_names
relabelling = \
map(lambda mn: ("%s_%s" % (p_name, mn),
"%s_%s" % (name, mn)),
all_entity_names)
else:
relabelling = [(p_name, name)]
mwe = ocaml.mwe_sibling(p_mwe, name, rename_prefix, relabelling)
self.mwes[name] = mwe
return mwe
logger.info("Building MWE %s" % name)
elems = self.elems_by_field[name]
mwe = ocaml.make_mwe(name, self.mesh.raw_mesh,
list(enumerate(elems)), [],
self.regions.properties_by_region)
self.mwes[name] = mwe
return mwe
def _simplify_operators(self):
"""Simplify the operators before building them."""
ops = self.computations._by_type.get('Operator', [])
op_names = ", ".join(map(Operator.get_name, ops))
logger.info("Simplifying operators: %s." % op_names)
simplify_context = \
OpSimplifyContext(quantities=self.quantities,
material=self.regions.all_entity_names)
for op in ops:
logger.debug("Simplifying operator %s" % op.name)
op.simplify(context=simplify_context)
def _build_operators(self):
ops = self.computations._by_type.get('Operator', [])
op_names = ", ".join(map(Operator.get_name, ops))
logger.info("Building operators: %s." % op_names)
operator_dict = {}
for op in ops:
logger.debug("Building operator %s" % op.name)
op_text = op.get_text()
mwe_in, mwe_out = op.get_inputs_and_outputs()
op_full_name = op.get_full_name()
assert len(mwe_in) == 1 and len(mwe_out) == 1, \
("Operators should only involve exactly one quantity as input "
"and one quantity as output. However, for operator '%s' "
"input=%s and output=%s." % (op.name, mwe_in, mwe_out))
operator_dict[op_full_name] = \
nlam.lam_operator(op_full_name, mwe_out[0], mwe_in[0], op_text)
# We should now register a VM call to compute the equation
logger.debug("Creating operator program for %s" % op.name)
v_in, v_out = ["v_%s" % name for name in mwe_in + mwe_out]
op.add_commands(["SM*V", op_full_name, v_in, v_out])
if op.cofield_to_field:
op.add_commands(["CFBOX", mwe_out[0], v_out])
self._built["Operator"] = True
return operator_dict
def _build_ksps(self):
ksps = self.computations._by_type.get('KSP', [])
ksp_dict = {}
for ksp in ksps:
ksp_full_name = ksp.get_full_name()
ksp_dict[ksp_full_name] = ksp._build_lam_object(self)
self._built["KSP"] = True
return ksp_dict
def _build_bems(self):
bems = self.computations._by_type.get('BEM', [])
bem_dict = {}
for bem in bems:
bem_full_name = bem.get_full_name()
bem_dict[bem_full_name] = bem._build_lam_object(self)
return bem_dict
def _simplify_equations(self):
"""Simplify the equations before building them."""
eqs = self.computations._by_type.get('Equation', [])
eq_names = ", ".join(map(Equation.get_name, eqs))
logger.info("Simplifying equations: %s." % eq_names)
simplify_context = \
EqSimplifyContext(quantities=self.quantities,
material=self.regions.all_entity_names)
for eq in eqs:
logger.debug("Simplifying equation %s" % eq.name)
eq.simplify(context=simplify_context)
def _own_ccodes(self):
# Call the own methods of all the CCodes objects in the Model.
ccodes = self.computations._by_type.get('CCode', [])
ccodes_names = ", ".join(map(CCode.get_name, ccodes))
logger.info("Get ownership of C-codes: %s." % ccodes_names)
for ccode in ccodes:
logger.debug("Getting ownership of ccode '%s'" % ccode.name)
ccode.own(self)
def _build_equations(self):
eqs = self.computations._by_type.get('Equation', [])
eq_names = ", ".join(map(Equation.get_name, eqs))
logger.info("Building equations: %s." % eq_names)
equation_dict = {}
for eq in eqs:
logger.debug("Building equation %s" % eq.name)
eq_full_name = eq.get_full_name()
equation_dict[eq_full_name] = eq._build_lam_object(self)
# We should now register a VM call to compute the equation
logger.debug("Creating equation program for %s" % eq.name)
fields = ["v_%s" % name for name in eq.get_all_quantities()]
eq.add_commands(["SITE-WISE-IPARAMS", eq_full_name, fields, []])
self._built["Equations"] = True
return equation_dict
def _build_ccodes(self):
ccodes = self.computations._by_type.get('CCode', [])
ccode_dict = {}
for ccode in ccodes:
logger.debug("Building ccode %s" % ccode.name)
ccode_full_name = ccode.get_full_name()
ccode_dict[ccode_full_name] = ccode._build_lam_object(self)
# We should now register a VM call to launch the CCode
logger.info("Creating ccode program for %s" % ccode.name)
fields = ["v_%s" % name for name in ccode.get_all_quantities()]
ccode.add_commands(["SITE-WISE-IPARAMS", ccode_full_name, fields, []])
self._built["CCode"] = True
return ccode_dict
def _build_programs(self):
progs = (self.computations._by_type.get('LAMProgram', [])
+ self.computations._by_type.get('CCode', [])
+ self.computations._by_type.get('Equation', [])
+ self.computations._by_type.get('Operator', []))
prog_names = ", ".join(map(LAMProgram.get_prog_name, progs))
logger.info("Building programs: %s." % prog_names)
prog_dict = {}
for prog in progs:
prog_name = prog.get_prog_name()
logger.debug("Building program %s" % prog_name)
prog_dict[prog_name] = prog._build_lam_program()
self._built["LAMPrograms"] = True
return prog_dict
def _depend(self, q1_name, q2_name):
"""Return whether the quantity q1_name depends on the quantity
q2_name."""
if q1_name in self.quantities.dependencies:
op, input_qs = self.quantities.dependencies[q1_name]
for input_q in input_qs:
if input_q == q2_name:
return True
elif self._depend(input_q, q2_name):
return True
return False
def _depend_path(self, q1_name, q2_name):
"""Return whether the quantity q1_name depends on the quantity
q2_name."""
if q1_name in self.quantities.dependencies:
op, input_qs = self.quantities.dependencies[q1_name]
for input_q in input_qs:
if input_q == q2_name:
return "%s ==(%s)==> %s" % (q2_name, op.name, q1_name)
else:
s = self._depend(input_q, q2_name)
if s:
return "%s ==(%s)==> %s" % (s, op.name, q1_name)
return ""
def _build_dependency_tree(self):
# Determine dependencies and involved quantities
q_dependencies = {}
involved_qs = {}
for computation in self.computations._all:
if computation.auto_dep:
# Compute automatically the dependencies
inputs, outputs = computation.get_inputs_and_outputs()
for o in outputs:
q_dependencies[o] = (computation, inputs)
for q_name in inputs + outputs:
if not q_name in involved_qs:
involved_qs[q_name] = None
# Determine primary quantities
derived_qs = []
primary_qs = []
for q_name in involved_qs:
if q_name in q_dependencies:
derived_qs.append(q_name)
else:
primary_qs.append(q_name)
self.quantities.primary = primary_qs
self.quantities.derived = derived_qs
self.quantities.dependencies = q_dependencies
# Cecking for circular dependencies
for derived_q in derived_qs:
if self._depend(derived_q, derived_q):
# does the quantity derived_q depend on itself
dep_path = self._depend_path(derived_q, derived_q)
raise NsimModelError("Circular dependency detected for %s: %s"
% (derived_q, dep_path))
self._built["DepTree"] = True
def _check_model_obj(self, obj):
if not isinstance(obj, ModelObj):
raise ValueError("The object you provided is not a ModelObj")
if obj.model != self:
raise ValueError("The object you provided has does not belong "
"to this Model.")
def declare_target(self, *targets):
"""Declare the targets of the model, or - in other words - what
objects the user wants to use. This will help the system to find out
which parts of the model are unnecessary and can be removed.
The system will examine the provided targets and find out which
quantities and computations are needed in order to compute them.
It will then remove the remanining objects in the model.
If this method is not used, then all the model object are kept."""
for target in targets:
self._check_model_obj(target)
self.targets.extend(targets)
def collect_required_objects(self, targets, bag={}, req_by="?"):
"""Collect the Model objects required by the given model objects
(provided in targets)."""
for target in targets:
tfn = target.get_full_name()
if tfn in bag:
continue
logger.debug("collect_required_objects: %s required by %s"
% (tfn, req_by))
bag[tfn] = target
if isinstance(target, Computation):
all_q_names = target.get_all_quantities()
all_qs = map(self.quantities.__getitem__, all_q_names)
self.collect_required_objects(all_qs, bag=bag, req_by=tfn)
sub_comps = target.get_required_computations()
self.collect_required_objects(sub_comps, bag=bag, req_by=tfn)
elif isinstance(target, Quantity):
computation_and_inputs = \
self.quantities.dependencies.get(target.name, None)
if computation_and_inputs != None:
computation = computation_and_inputs[0]
self.collect_required_objects([computation], bag=bag,
req_by=tfn)
elif isinstance(target, Timestepper):
qs = map(self.quantities.__getitem__, target.x + target.dxdt)
self.collect_required_objects(qs, bag=bag, req_by=tfn)
else:
raise NsimModelError("Unknown model object (%s)"
% type(target))
return bag
def _remove_unused(self, targets):
required_objects = self.collect_required_objects(targets)
# Remove unused computations
all_computations = list(self.computations._all)
removed_computations = []
for computation in all_computations:
fn = computation.get_full_name()
if fn not in required_objects:
removed_computations.append(computation)
self.computations.pop(computation)
if removed_computations:
c_names = \
", ".join(map(Computation.get_name, removed_computations))
logger.info("Removed unused computations: %s." % c_names)
# Remove quantities (except Constant quantities)
all_quantities = list(self.quantities._all)
removed_quantities = []
for quantity in all_quantities:
if not isinstance(quantity, Constant):
fn = quantity.get_full_name()
if fn not in required_objects:
removed_quantities.append(quantity)
self.quantities.pop(quantity)
if removed_quantities:
q_names = ", ".join(map(Quantity.get_name, removed_quantities))
logger.info("Removed unused quantities: %s." % q_names)
def write_dependency_tree(self, out=sys.stdout):
"""Write to the provided stream (sys.stdout, if not provided)
information about the inferred dependency tree between quantities
and operators."""
out.write("Primary quantities: %s\n" % self.quantities.primary)
out.write("Derived quantities: %s\n" % self.quantities.derived)
out.write("Dependencies (as INPUTS==[COMPUTATION]==>OUTPUT):\n")
ds = self.quantities.dependencies
for o in ds:
c, i = ds[o]
out.write("%s ==(%s)==> %s\n" % (i, c.name, o))
def write_debug_info(self, out=sys.stdout):
def write_section(s):
out.write("\n%s\n%s\n\n" % (s, len(s)*"-"))
write_section("Dependency tree:")
self.write_dependency_tree(out)
write_section("Equations:")
for computation in self.computations._all:
out.write("%s\n\n" % computation.get_desc())
def _build_target_maker(self, target, primaries={}, targets_to_make=[]):
assert self._was_built("DepTree"), \
"The target-maker builder can be used only after building the " \
"dependency tree!"
if not target in self.quantities.dependencies:
primaries[target] = primaries.get(target, 0) + 1
else:
computation, inputs = self.quantities.dependencies[target]
for i in inputs:
self._build_target_maker(i, primaries, targets_to_make)
targets_to_make.append(computation)
def _build_timesteppers(self):
nlam_tss = {}
simplify_context = \
EqSimplifyContext(quantities=self.quantities,
material=self.regions.all_entity_names)
for ts in self.timesteppers._all:
nr_primary_fields = len(ts.x)
assert nr_primary_fields == len(ts.dxdt)
inputs, outputs = \
ts.eq_for_jacobian.get_inputs_and_outputs(context=simplify_context)
all_names = inputs + outputs
x_and_dxdt = ts.x + ts.dxdt
if contains_all(outputs, ts.dxdt):
other_names = [name
for name in all_names
if name not in x_and_dxdt]
else:
print ts.dxdt, outputs
eq = ts.eq_for_jacobian
msg = ("Jacobian for timestepper %s (x=%s and dxdt=%s) does "
"not determine the value of dxdt. The Jacobian is "
"%s, which was simplified from: %s."
% (ts.name, ts.x, ts.dxdt,
eq.simplified_tree, eq.text))
raise ValueError(msg)
# List of all quantities involved in jacobi equation
all_names = x_and_dxdt + other_names
# Build a dictionary containing info about how to derive each
# quantity
how_to_derive = {}
if ts.derivatives != None:
for quant, way in ts.derivatives:
if isinstance(way, Operator):
op_full_name = way.get_full_name()
how_to_derive[quant.name] = ("OPERATOR", op_full_name)
else:
raise ValueError("Timestepper was build specifying "
"that %s should be used to compute the derivative "
"of %s, but only operators can be used at the "
"moment." % (quant.name, way.name))
all_v_names = ["v_%s" % name for name in all_names]
derivs = [("PRIMARY", "")]*(2*nr_primary_fields)
for name in other_names:
if name in how_to_derive:
derivs.append(how_to_derive[name])
else:
derivs.append(("IGNORE", ""))
# Build dxdt update program
primaries = {}
targets_to_make = []
for dxdt in ts.dxdt:
self._build_target_maker(dxdt, primaries, targets_to_make)
if False:
print "In order to update the RHS I have to:"
for p in primaries:
print "distribute quantity %s" % p
for t in targets_to_make:
print "run computation %s" % t.name
raw_input()
dxdt_updater = LAMProgram("TsUp_%s" % ts.name)
for t in targets_to_make:
dxdt_updater.add_commands(["GOSUB", t.get_prog_name()])
self.computations.add(dxdt_updater)
assert not self._was_built("LAMPrograms"), \
"Timesteppers should be built before LAM programs!"
full_name = ts.get_full_name()
nlam_ts = \
nlam.lam_timestepper(full_name,
all_names,
all_v_names,
dxdt_updater.get_full_name(),
nr_primary_fields=nr_primary_fields,
name_jacobian=None,
pc_rtol=ts.pc_rtol,
pc_atol=ts.pc_atol,
max_order=ts.max_order,
krylov_max=ts.krylov_max,
jacobi_eom=ts.eq_for_jacobian.get_text(),
phys_field_derivs=derivs,
jacobi_prealloc_diagonal=
ts.jacobi_prealloc_diagonal,
jacobi_prealloc_off_diagonal=
ts.jacobi_prealloc_off_diagonal)
nlam_tss[full_name] = nlam_ts
self._built["TSs"] = True
return nlam_tss
def _build_lam(self, remove_unused=None):
# Carry out equation and operator simplifications
self._simplify_operators()
self._simplify_equations()
self._own_ccodes()
# Build the dependency tree
self._build_dependency_tree()
# Remove unused objects, if required
if (remove_unused is True
or (remove_unused is None and len(self.targets) > 0)):
self._remove_unused(self.targets)
# First build all the elements
field_quants = self.quantities._by_type.get('SpaceField', [])
field_quants += self.quantities._by_type.get('SpaceTimeField', [])
param_quants = self.quantities._by_type.get('TimeField', [])
for field_quant in field_quants:
self._build_elems(field_quant.name,
field_quant.shape,
on_material=field_quant.def_on_mat)
# Now build all the MWEs
for field_quant in field_quants:
self._build_mwe(field_quant.name)
# Build the simplified operators
operators = self._build_operators()
equations = self._build_equations()
bems = self._build_bems()
ksps = self._build_ksps()
ccodes = self._build_ccodes()
jacobi = {} # Not used (should clean this)
timesteppers = self._build_timesteppers()
programs = self._build_programs()
debugfile = None
# Build LAM vector dictionary
vectors = {}
for mwe_name in self.mwes.copy():
vec_name = "v_%s" % mwe_name
assert not vec_name in vectors, \
"Duplicate definition of vector '%s'" % vec_name
quantity = self.quantities[mwe_name]
vectors[vec_name] = \
nlam.lam_vector(name=vec_name, mwe_name=mwe_name,
restriction=quantity.restrictions)
lam = nlam.make_lam(self.name,
intensive_params=self.intensive_params,
mwes=self.mwes.values(),
vectors=vectors.values(),
operators=operators.values(),
bem_matrices=bems.values(),
ksps=ksps.values(),
local_operations=(equations.values()
+ ccodes.values()),
jacobi_plans=jacobi.values(),
programs=programs.values(),
timesteppers=timesteppers.values(),
lam_debugfile=debugfile)
self.lam = lam
def _vivify_objs(self, lam):
logger.info("Vivifiying fields...")
field_quants = (self.quantities._by_type.get('SpaceField', [])
+ self.quantities._by_type.get('SpaceTimeField', []))
for q in field_quants:
q.vivify(self)
logger.info("Vivifiying timesteppers...")
for ts in self.timesteppers._all:
ts.vivify(self)
logger.info("Vivifiying computations...")
for eq in self.computations._all:
eq.vivify(self)
def build(self):
self._build_lam()
self._vivify_objs(self.lam)
self._built["LAM"] = True