def __init__(self, var, name=''):
CellVariable.__init__(self,
mesh=var.mesh,
name=name,
elementshape=(var.mesh.dim, ) + var.shape[:-1])
self.var = self._requires(var)
self.faceGradientContributions = _FaceGradContributions(self.var)
def __init__(self, faceVariable, mesh = None):
if not mesh:
mesh = faceVariable.getMesh()
CellVariable.__init__(self, mesh, hasOld = 0)
self.faceVariable = self._requires(faceVariable)
def __init__(self, mesh, name = '', value = 0., unit = None, hasOld = 0, narrowBandWidth = 1e+10):
"""
Creates a `distanceVariable` object.
:Parameters:
- `mesh`: The mesh that defines the geometry of this variable.
- `name`: The name of the variable.
- `value`: The initial value.
- `unit`: the physical units of the variable
- `hasOld`: Whether the variable maintains an old value.
- `narrowBandWidth`: The width of the region about the zero level set
within which the distance function is evaluated.
"""
CellVariable.__init__(self, mesh, name = name, value = value, unit = unit, hasOld = hasOld)
self._markStale()
self.narrowBandWidth = narrowBandWidth
self.cellToCellDistances = MA.filled(self.mesh._getCellToCellDistances(), 0)
self.cellNormals = MA.filled(self.mesh._getCellNormals(), 0)
self.cellAreas = MA.filled(self.mesh._getCellAreas(), 0)
## self.cellToCellDistances = numerix.array(MA.array(self.mesh._getCellToCellDistances()).filled(0))
## self.cellNormals = numerix.array(MA.array(self.mesh._getCellNormals()).filled(0))
## self.cellAreas = numerix.array(MA.array(self.mesh._getCellAreas()).filled(0))
self.cellToCellIDs = numerix.array(self.mesh._getCellToCellIDsFilled())
self.adjacentCellIDs = self.mesh._getAdjacentCellIDs()
self.exteriorFaces = self.mesh.getExteriorFaces()
self.cellFaceIDs = self.mesh._getCellFaceIDs()
def __init__(self, distanceVar, bulkVar, rateConstant):
CellVariable.__init__(self, mesh = distanceVar.getMesh())
self.distanceVar = self._requires(distanceVar)
self.bulkVar = self._requires(bulkVar)
self.rateConstant = rateConstant
self.dt = 0
def __init__(self, value = 0., distanceVar = None, name = 'surfactant variable', hasOld=False):
"""
A simple 1D test:
>>> from fipy.meshes.grid1D import Grid1D
>>> mesh = Grid1D(dx = 1., nx = 4)
>>> from fipy.models.levelSet.distanceFunction.distanceVariable \\
... import DistanceVariable
>>> distanceVariable = DistanceVariable(mesh = mesh,
... value = (-1.5, -0.5, 0.5, 941.5))
>>> surfactantVariable = SurfactantVariable(value = 1,
... distanceVar = distanceVariable)
>>> print numerix.allclose(surfactantVariable, (0, 0., 1., 0))
1
A 2D test case:
>>> from fipy.meshes.grid2D import Grid2D
>>> mesh = Grid2D(dx = 1., dy = 1., nx = 3, ny = 3)
>>> distanceVariable = DistanceVariable(mesh = mesh,
... value = (1.5, 0.5, 1.5,
... 0.5,-0.5, 0.5,
... 1.5, 0.5, 1.5))
>>> surfactantVariable = SurfactantVariable(value = 1,
... distanceVar = distanceVariable)
>>> print numerix.allclose(surfactantVariable, (0, 1, 0, 1, 0, 1, 0, 1, 0))
1
Another 2D test case:
>>> mesh = Grid2D(dx = .5, dy = .5, nx = 2, ny = 2)
>>> distanceVariable = DistanceVariable(mesh = mesh,
... value = (-0.5, 0.5, 0.5, 1.5))
>>> surfactantVariable = SurfactantVariable(value = 1,
... distanceVar = distanceVariable)
>>> print numerix.allclose(surfactantVariable,
... (0, numerix.sqrt(2), numerix.sqrt(2), 0))
1
:Parameters:
- `value`: The initial value.
- `distanceVar`: A `DistanceVariable` object.
- `name`: The name of the variable.
"""
CellVariable.__init__(self, mesh = distanceVar.getMesh(), name = name, hasOld=False)
self.distanceVar = self._requires(distanceVar)
self.value = distanceVar.getCellInterfaceAreas() * value / self.mesh.getCellVolumes()
if hasOld:
self.old = self.copy()
else:
self.old = None
self.interfaceSurfactantVariable = None
def __init__(self, faceVariable, mesh=None):
if not mesh:
mesh = faceVariable.mesh
CellVariable.__init__(self,
mesh,
hasOld=0,
elementshape=faceVariable.shape[:-1])
self.faceVariable = self._requires(faceVariable)
def __init__(self, distanceVar):
"""
Creates an `_InterfaceAreaVariable` object.
Parameters
----------
distanceVar : ~fipy.variables.distanceVariable.DistanceVariable
"""
CellVariable.__init__(self, distanceVar.mesh, hasOld=False)
self.distanceVar = self._requires(distanceVar)
def __init__(self, distanceVar):
"""
Creates an `_InterfaceAreaVariable` object.
:Parameters:
- `distanceVar` : A `DistanceVariable` object.
"""
CellVariable.__init__(self, distanceVar.mesh, hasOld=False)
self.distanceVar = self._requires(distanceVar)
def __init__(self, distanceVar):
"""
Creates an `_InterfaceFlagVariable` object.
:Parameters:
- `distanceVar` : A `DistanceVariable` object.
"""
CellVariable.__init__(self, distanceVar.mesh, hasOld=False)
self.distanceVar = self._requires(distanceVar)
def __init__(self, distribution, dx = 1., nx = None, offset = 0.):
r"""
Produces a histogram of the values of the supplied distribution.
:Parameters:
- `distribution`: The collection of values to sample.
- `dx`: the bin size
- `nx`: the number of bins
- `offset`: the position of the first bin
"""
CellVariable.__init__(self, mesh = Grid1D(dx = dx, nx = nx) + (offset,))
self.distribution = self._requires(distribution)
def __init__(self, mesh, name = '', value = 0., unit = None, hasOld = 0):
"""
Creates a `distanceVariable` object.
:Parameters:
- `mesh`: The mesh that defines the geometry of this variable.
- `name`: The name of the variable.
- `value`: The initial value.
- `unit`: the physical units of the variable
- `hasOld`: Whether the variable maintains an old value.
"""
CellVariable.__init__(self, mesh, name = name, value = value, unit = unit, hasOld = hasOld)
self._markStale()
def __init__(self, mesh, name = '', value = 0., unit = None, hasOld = 0):
"""
Creates a `distanceVariable` object.
:Parameters:
- `mesh`: The mesh that defines the geometry of this variable.
- `name`: The name of the variable.
- `value`: The initial value.
- `unit`: the physical units of the variable
- `hasOld`: Whether the variable maintains an old value.
"""
CellVariable.__init__(self, mesh, name = name, value = value, unit = unit, hasOld = hasOld)
self._markStale()
def __init__(self, ionVar = None, distanceVar = None, depositionRate = None, metalIonMolarVolume = None):
"""
Creates a `_MetalIonSourceVariable` object.
:Parameters:
- `ionVar` : The metal ion concentration.
- `distanceVar` : A `DistanceVariable` object.
- `depositionRate` : The deposition rate.
- `metalIonMolarVolume` : Molar volume of the metal ions.
"""
CellVariable.__init__(self, distanceVar.getMesh(), hasOld = 0)
self.ionVar = self._requires(ionVar)
self.distanceVar = self._requires(distanceVar)
self.depositionRate = self._requires(depositionRate)
self.metalIonMolarVolume = metalIonMolarVolume
def __init__(self, distribution, dx=1., nx=None, offset=0.):
r"""
Produces a histogram of the values of the supplied distribution.
Parameters
----------
distribution : array_like or ~fipy.variables.Variable
The collection of values to sample.
dx : float
The bin size
nx : int
The number of bins
offset : float
The position of the first bin
"""
CellVariable.__init__(self, mesh=Grid1D(dx=dx, nx=nx) + (offset, ))
self.distribution = self._requires(distribution)
def __init__(self, mesh, name = '', value = 0., unit = None, hasOld = 0):
"""
Creates a `distanceVariable` object.
Parameters
----------
mesh : ~fipy.meshes.mesh.Mesh
The mesh that defines the geometry of this variable.
name : str
The name of the variable.
value : float or array_like
The initial value.
unit : str or ~fipy.tools.dimensions.physicalField.PhysicalUnit
The physical units of the variable
hasOld : bool
Whether the variable maintains an old value.
"""
CellVariable.__init__(self, mesh, name = name, value = value, unit = unit, hasOld = hasOld)
self._markStale()
def __init__(self, var, name = ''):
CellVariable.__init__(self, mesh=var.getMesh(), name=name, rank=var.getRank() + 1)
self.var = self._requires(var)
def __init__(self, modVar):
CellVariable.__init__(self, mesh = modVar.getMesh())
self.modVar = self._requires(modVar)
def __init__(self, modVar):
CellVariable.__init__(self, mesh=modVar.mesh)
self.modVar = self._requires(modVar)
def __init__(self, rateConstant = None, distanceVar = None):
CellVariable.__init__(self, mesh = distanceVar.getMesh())
self.distanceVar = self._requires(distanceVar)
self.rateConstant = rateConstant
def __init__(self, var, name=''):
CellVariable.__init__(self, mesh=var.mesh, name=name, elementshape=(var.mesh.dim,) + var.shape[:-1])
self.var = self._requires(var)
self.faceGradientContributions = _FaceGradContributions(self.var)
def __init__(self, faceVariable, mesh = None):
if not mesh:
mesh = faceVariable.mesh
CellVariable.__init__(self, mesh, hasOld = 0, elementshape=faceVariable.shape[:-1])
self.faceVariable = self._requires(faceVariable)
def __init__(self, var, name = ''):
CellVariable.__init__(self, mesh=var.mesh, name=name, rank=var.rank + 1)
self.var = self._requires(var)
def __init__(self, surfactantVar):
CellVariable.__init__(self, name = surfactantVar.name + "_interface", mesh = surfactantVar.mesh)
self.surfactantVar = self._requires(surfactantVar)
def __init__(self, mesh, name='', hasOld=0):
if self.__class__ is NoiseVariable:
raise NotImplementedError, "can't instantiate abstract base class"
CellVariable.__init__(self, mesh=mesh, name=name, hasOld=hasOld)
self.scramble()
def __init__(self, var = None, name = ''):
CellVariable.__init__(self, mesh = mesh.getFineMesh(), name = name)
self.var = self._requires(var)
def __init__(self, mesh, name = '', hasOld = 0):
if self.__class__ is NoiseVariable:
raise NotImplementedError, "can't instantiate abstract base class"
CellVariable.__init__(self, mesh = mesh, name = name, hasOld = hasOld)
self.scramble()
def __init__(self, surfactantVar):
CellVariable.__init__(self,
name=surfactantVar.name + "_interface",
mesh=surfactantVar.mesh)
self.surfactantVar = self._requires(surfactantVar)
def __init__(self, var, name=""):
CellVariable.__init__(self, mesh=var.mesh, name=name, rank=var.rank + 1)
self.var = self._requires(var)
def __init__(self,
value=0.,
distanceVar=None,
name='surfactant variable',
hasOld=False):
"""
A simple 1D test:
>>> from fipy.meshes import Grid1D
>>> mesh = Grid1D(dx = 1., nx = 4)
>>> from fipy.variables.distanceVariable import DistanceVariable
>>> distanceVariable = DistanceVariable(mesh = mesh,
... value = (-1.5, -0.5, 0.5, 941.5))
>>> surfactantVariable = SurfactantVariable(value = 1,
... distanceVar = distanceVariable)
>>> print(numerix.allclose(surfactantVariable, (0, 0., 1., 0)))
1
A 2D test case:
>>> from fipy.meshes import Grid2D
>>> mesh = Grid2D(dx = 1., dy = 1., nx = 3, ny = 3)
>>> distanceVariable = DistanceVariable(mesh = mesh,
... value = (1.5, 0.5, 1.5,
... 0.5, -0.5, 0.5,
... 1.5, 0.5, 1.5))
>>> surfactantVariable = SurfactantVariable(value = 1,
... distanceVar = distanceVariable)
>>> print(numerix.allclose(surfactantVariable, (0, 1, 0, 1, 0, 1, 0, 1, 0)))
1
Another 2D test case:
>>> mesh = Grid2D(dx = .5, dy = .5, nx = 2, ny = 2)
>>> distanceVariable = DistanceVariable(mesh = mesh,
... value = (-0.5, 0.5, 0.5, 1.5))
>>> surfactantVariable = SurfactantVariable(value = 1,
... distanceVar = distanceVariable)
>>> print(numerix.allclose(surfactantVariable,
... (0, numerix.sqrt(2), numerix.sqrt(2), 0)))
1
:Parameters:
- `value`: The initial value.
- `distanceVar`: A `DistanceVariable` object.
- `name`: The name of the variable.
"""
CellVariable.__init__(self,
mesh=distanceVar.mesh,
name=name,
hasOld=False)
self.distanceVar = self._requires(distanceVar)
self._value = numerix.array(
distanceVar.cellInterfaceAreas) * value / self.mesh.cellVolumes
if hasOld:
self._old = self.copy()
else:
self._old = None
self.interfaceSurfactantVariable = None
def __init__(self, var=None, name=''):
CellVariable.__init__(self,
mesh=mesh.getFineMesh(),
name=name)
self.var = self._requires(var)
def __init__(self, var, name=""):
CellVariable.__init__(self, mesh=var.getMesh(), name=name, rank=var.getRank() + 1)
self.var = self._requires(var)
self.faceGradientContributions = _FaceGradContributions(self.var)
def __init__(self, distanceVar, vars = ()):
CellVariable.__init__(self, mesh = distanceVar.getMesh())
self.vars = vars
for var in self.vars:
self._requires(var)
self.distanceVar = self._requires(distanceVar)
