def __init__(self, name, inputs=None, outputs=None, internals=None,
auto_dep=None):
ModelObj.__init__(self, name)
self.inputs = inputs
self.outputs = outputs
self.internals = internals
self.auto_dep = auto_dep if auto_dep != None else True
def __init__(self,
name,
inputs=None,
outputs=None,
internals=None,
auto_dep=None):
ModelObj.__init__(self, name)
self.inputs = inputs
self.outputs = outputs
self.internals = internals
self.auto_dep = auto_dep if auto_dep != None else True
def vivify(self, model):
ModelObj.vivify(self, model)
vols = model.mesh.regionvolumes
if self.subfields == False:
self.volumes = {self.name: sum(vols[1:])}
else:
if self.subfields == True:
self.subfields = model.regions.all_entity_names
# Calculate the volume per subfield as the sum of the volumes
# where the subfield is defined
self.volumes = volumes = {}
for subfield in self.subfields:
volumes["%s_%s" % (self.name, subfield)] = reduce(
lambda v, region_idx: v + vols[region_idx], model.regions.regions_by_entity[subfield], 0.0
)
def vivify(self, model):
ModelObj.vivify(self, model)
vols = model.mesh.regionvolumes
if self.subfields == False:
self.volumes = {self.name: sum(vols[1:])}
else:
if self.subfields == True:
self.subfields = model.regions.all_entity_names
# Calculate the volume per subfield as the sum of the volumes
# where the subfield is defined
self.volumes = volumes = {}
for subfield in self.subfields:
volumes["%s_%s" % (self.name, subfield)] = \
reduce(lambda v, region_idx: v + vols[region_idx],
model.regions.regions_by_entity[subfield], 0.0)
def __init__(self, name, x, dxdt,
eq_for_jacobian=None, time_unit=None,
derivatives=None,
pc_rtol=1e-2, pc_atol=1e-7, pc_dtol=None, pc_maxits=1000000,
rtol=1e-5, atol=1e-5, initial_time=0.0,
max_order=2, krylov_max=300,
jacobi_prealloc_diagonal=75,
jacobi_prealloc_off_diagonal=45):
ModelObj.__init__(self, name)
if (eq_for_jacobian != None
and not isinstance(eq_for_jacobian, Equation)):
raise ValueError("The optional argument eq_for_jacobian should be"
"set to an instance of the Equation class.")
if isinstance(x, str):
x = [x]
if isinstance(dxdt, str):
dxdt = [dxdt]
if len(x) != len(dxdt):
raise ValueError("x and dxdt should be lists with the same number "
"of entries.")
self.derivatives = derivatives
self.time_unit = time_unit
self.x = x
self.dxdt = dxdt
self.eq_for_jacobian = eq_for_jacobian
self.rtol = rtol
self.atol = atol
self.pc_rtol = pc_rtol
self.pc_atol = pc_atol
self.pc_dtol = pc_dtol
self.pc_maxits = pc_maxits
self.initial_time = initial_time
self.max_order = max_order
self.krylov_max = krylov_max
self.jacobi_prealloc_diagonal = jacobi_prealloc_diagonal
self.jacobi_prealloc_off_diagonal = jacobi_prealloc_off_diagonal
self.initialised = False
self.need_reinitialise = True
def __init__(self, name, shape=[], value=None, unit=None, subfields=False):
"""Define a new quantity:
name: name of the quantity (should be different for each quantity)
shape: shape. Examples: [] for scalars, [3] 3-component vectors, etc
value: initial value of the quantity. An initial value should be
provided only if the quantity is primary.
unit: the unit used for the quantity. Values will be stored in terms
of unit. For example, if unit=100 and you set the Quantity
to 200, then - internally - 2 will be used.
subfields:
For each region specifies which subfield of the Quantity are
present in it. Example: [["s1", "s2"], ["s1"], []] means
that the field has two subfields "s1" and "s2" in the region
with index 0, only "s1" in region with index 2, and is not
defined in region 3. If subfield is set to False, then the
field doesn't have any subfields. If it is set to True than
it gets all the default subfields of the model.
"""
ModelObj.__init__(self, name)
self.shape = shape # Shape of the field
self.value = None # Value (instance of Value class)
self.unit = unit # Unit
self.subfields = subfields
if subfields not in [True, False]:
raise NotImplementedError(
"User defined subfield allocations are "
"not permitted, yet. Use only "
"subfields=False or subfields=True "
"when instantiating a new Quantity."
)
self.def_on_mat = subfields
self.regions = None # self.regions[sf_name] is the list of regions
# indices where the subfield sf_name is defined
self.volumes = None # self.volumes[sf_name] is the sum of volumes
# of all the regions self.regions[sf_name].
self.is_primary = True # unused at the moment
self.set_value(value)
def __init__(self, name, shape=[], value=None, unit=None, subfields=False):
"""Define a new quantity:
name: name of the quantity (should be different for each quantity)
shape: shape. Examples: [] for scalars, [3] 3-component vectors, etc
value: initial value of the quantity. An initial value should be
provided only if the quantity is primary.
unit: the unit used for the quantity. Values will be stored in terms
of unit. For example, if unit=100 and you set the Quantity
to 200, then - internally - 2 will be used.
subfields:
For each region specifies which subfield of the Quantity are
present in it. Example: [["s1", "s2"], ["s1"], []] means
that the field has two subfields "s1" and "s2" in the region
with index 0, only "s1" in region with index 2, and is not
defined in region 3. If subfield is set to False, then the
field doesn't have any subfields. If it is set to True than
it gets all the default subfields of the model.
"""
ModelObj.__init__(self, name)
self.shape = shape # Shape of the field
self.value = None # Value (instance of Value class)
self.unit = unit # Unit
self.subfields = subfields
if subfields not in [True, False]:
raise NotImplementedError("User defined subfield allocations are "
"not permitted, yet. Use only "
"subfields=False or subfields=True "
"when instantiating a new Quantity.")
self.def_on_mat = subfields
self.regions = None # self.regions[sf_name] is the list of regions
# indices where the subfield sf_name is defined
self.volumes = None # self.volumes[sf_name] is the sum of volumes
# of all the regions self.regions[sf_name].
self.is_primary = True # unused at the moment
self.set_value(value)
