Tree Mesh¶

class
discretize.
TreeMesh
(h, x0=None, **kwargs)[source]¶ Bases:
discretize.tree_ext._TreeMesh
,discretize.TensorMesh.BaseTensorMesh
,discretize.InnerProducts.InnerProducts
,discretize.MeshIO.TreeMeshIO
Required Properties:
 axis_u (
Vector3
): Vector orientation of udirection. For more details see the docs for therotation_matrix
property., a 3D Vector of <class ‘float’> with shape (3), Default: X  axis_v (
Vector3
): Vector orientation of vdirection. For more details see the docs for therotation_matrix
property., a 3D Vector of <class ‘float’> with shape (3), Default: Y  axis_w (
Vector3
): Vector orientation of wdirection. For more details see the docs for therotation_matrix
property., a 3D Vector of <class ‘float’> with shape (3), Default: Z  h (a list of
Array
): h is a list containing the cell widths of the tensor mesh in each dimension., a list (each item is a list or numpy array of <class ‘float’> with shape (*)) with length between 0 and 3  reference_system (
String
): The type of coordinate reference frame. Can take on the values cartesian, cylindrical, or spherical. Abbreviations of these are allowed., a unicode string, Default: cartesian  x0 (
Array
): origin of the mesh (dim, ), a list or numpy array of <class ‘float’> with shape (*)

vntF
¶

vntE
¶

cellGradStencil
¶

cellGrad
¶ Cell centered Gradient operator built off of the faceDiv operator. Grad =  (Mf)^{1} * Div * diag (volume)

cellGradx
¶ Cell centered Gradient operator in xdirection (Gradx) Grad = sp.vstack((Gradx, Grady, Gradz))

cellGrady
¶ Cell centered Gradient operator in ydirection (Gradx) Grad = sp.vstack((Gradx, Grady, Gradz))

cellGradz
¶ Cell centered Gradient operator in zdirection (Gradz) Grad = sp.vstack((Gradx, Grady, Gradz))

faceDivx
¶

faceDivy
¶

faceDivz
¶

permuteCC
¶

permuteF
¶

permuteE
¶

plotSlice
(v, vType='CC', normal='Z', ind=None, grid=True, view='real', ax=None, clim=None, showIt=False, pcolorOpts=None, streamOpts=None, gridOpts=None)[source]¶

area
¶

aveCC2F
¶

aveCC2Fx
¶

aveCC2Fy
¶ Construct the averaging operator on cell centers to cell yfaces.

aveCC2Fz
¶ Construct the averaging operator on cell centers to cell zfaces.

aveCCV2F
¶

aveE2CC
¶

aveE2CCV
¶

aveEx2CC
¶

aveEy2CC
¶

aveEz2CC
¶

aveF2CC
¶ Construct the averaging operator on cell faces to cell centers.

aveF2CCV
¶ Construct the averaging operator on cell faces to cell centers.

aveFx2CC
¶

aveFy2CC
¶

aveFz2CC
¶

aveN2CC
¶

aveN2E
¶ Construct the averaging operator on cell nodes to cell edges, keeping each dimension separate.

aveN2Ex
¶

aveN2Ey
¶

aveN2Ez
¶

aveN2F
¶ Construct the averaging operator on cell nodes to cell edges, keeping each dimension separate.

aveN2Fx
¶

aveN2Fy
¶

aveN2Fz
¶

axis_u
¶ axis_u (
Vector3
): Vector orientation of udirection. For more details see the docs for therotation_matrix
property., a 3D Vector of <class ‘float’> with shape (3), Default: X

axis_v
¶ axis_v (
Vector3
): Vector orientation of vdirection. For more details see the docs for therotation_matrix
property., a 3D Vector of <class ‘float’> with shape (3), Default: Y

axis_w
¶ axis_w (
Vector3
): Vector orientation of wdirection. For more details see the docs for therotation_matrix
property., a 3D Vector of <class ‘float’> with shape (3), Default: Z

cellBoundaryInd
¶

check_n_shape
(change)¶

check_x0
(change)¶

deserialize
(value, trusted=False, strict=False, assert_valid=False, **kwargs)¶ Creates HasProperties instance from serialized dictionary
This uses the Property deserializers to deserialize all JSONcompatible dictionary values into their corresponding Property values on a new instance of a HasProperties class. Extra keys in the dictionary that do not correspond to Properties will be ignored.
Parameters:
 value  Dictionary to deserialize new instance from.
 trusted  If True (and if the input dictionary has
'__class__'
keyword and this class is in the registry), the new HasProperties class will come from the dictionary. If False (the default), only the HasProperties class this method is called on will be constructed.  strict  Requires
'__class__'
, if present on the input dictionary, to match the deserialized instance’s class. Also disallows unused properties in the input dictionary. Default is False.  assert_valid  Require deserialized instance to be valid. Default is False.
 Any other keyword arguments will be passed through to the Property deserializers.

edge
¶

edgeCurl
¶

equal
(other)¶ Determine if two HasProperties instances are equivalent
Equivalence is determined by checking if all Property values on two instances are equal, using
Property.equal
.

faceBoundaryInd
¶

faceDiv
¶

fill
¶ How filled is the mesh compared to a TensorMesh? As a fraction: [0, 1].

finalize
()¶

getEdgeInnerProduct
(prop=None, invProp=False, invMat=False, doFast=True)¶ Parameters:  prop (numpy.ndarray) – material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 invProp (bool) – inverts the material property
 invMat (bool) – inverts the matrix
 doFast (bool) – do a faster implementation if available.
Return type: Returns: M, the inner product matrix (nE, nE)

getEdgeInnerProductDeriv
(prop, doFast=True, invProp=False, invMat=False)¶ Parameters:  prop (numpy.ndarray) – material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 doFast (bool) – do a faster implementation if available.
 invProp (bool) – inverts the material property
 invMat (bool) – inverts the matrix
Return type: Returns: dMdm, the derivative of the inner product matrix (nE, nC*nA)

getFaceInnerProduct
(prop=None, invProp=False, invMat=False, doFast=True)¶ Parameters:  prop (numpy.ndarray) – material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 invProp (bool) – inverts the material property
 invMat (bool) – inverts the matrix
 doFast (bool) – do a faster implementation if available.
Return type: Returns: M, the inner product matrix (nF, nF)

getFaceInnerProductDeriv
(prop, doFast=True, invProp=False, invMat=False)¶ Parameters:  prop (numpy.ndarray) – material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 doFast (bool) – do a faster implementation if available.
 invProp (bool) – inverts the material property
 invMat (bool) – inverts the matrix
Returns: dMdmu(u), the derivative of the inner product matrix (u)
Given u, dMdmu returns (nF, nC*nA)
Parameters: u (numpy.ndarray) – vector that multiplies dMdmu Return type: scipy.sparse.csr_matrix Returns: dMdmu, the derivative of the inner product matrix for a certain u

getInterpolationMat
()¶

getTensor
(key)¶ Returns a tensor list.
Parameters: key (str) – What tensor (see below) Return type: list Returns: list of the tensors that make up the mesh. key can be:
'CC' > scalar field defined on cell centers 'N' > scalar field defined on nodes 'Fx' > xcomponent of field defined on faces 'Fy' > ycomponent of field defined on faces 'Fz' > zcomponent of field defined on faces 'Ex' > xcomponent of field defined on edges 'Ey' > ycomponent of field defined on edges 'Ez' > zcomponent of field defined on edges

get_boundary_cells
()¶ Returns the indices of boundary cells in a given direction given an active index array.
Optional Input: :param numpy.array active_ind: None or Boolean array of active indexes in the mesh :param str direction: one of (‘zu’, ‘zd’, ‘xu’, ‘xd’, ‘yu’, ‘yd’)
Output: :rtype: numpy.array :return: Array of indices for the boundary cells in a given direction

gridCC
¶ Returns an M by N numpy array with the center locations of all cells in order. M is the number of cells and N=2,3 is the dimension of the mesh.

gridEx
¶

gridEy
¶

gridEz
¶

gridFx
¶

gridFy
¶

gridFz
¶

gridN
¶ Returns an M by N numpy array with the widths of all cells in order. M is the number of nodes and N=2,3 is the dimension of the mesh.

gridhEx
¶

gridhEy
¶

gridhEz
¶

gridhFx
¶

gridhFy
¶

gridhFz
¶

gridhN
¶

h
¶ h (a list of
Array
): h is a list containing the cell widths of the tensor mesh in each dimension., a list (each item is a list or numpy array of <class ‘float’> with shape (*)) with length between 0 and 3

h_gridded
¶ Returns an (nC, dim) numpy array with the widths of all cells in order

hx
¶ Width of cells in the x direction

hy
¶ Width of cells in the y direction

hz
¶ Width of cells in the z direction

insert_cells
()¶

isInside
(pts, locType='N')¶ Determines if a set of points are inside a mesh.
Parameters: pts (numpy.ndarray) – Location of points to test Return type: numpy.ndarray Returns: inside, numpy array of booleans

maxLevel
¶ The maximum level used, which may be less than levels.

max_level
¶

nC
¶

nE
¶

nEx
¶

nEy
¶

nEz
¶

nF
¶

nFx
¶

nFy
¶

nFz
¶

nN
¶

nhE
¶

nhEx
¶

nhEy
¶

nhEz
¶

nhF
¶

nhFx
¶

nhFy
¶

nhFz
¶

nhN
¶

nodalGrad
¶

normals
¶ Face Normals
Return type: numpy.ndarray Returns: normals, (sum(nF), dim)

ntE
¶

ntEx
¶

ntEy
¶

ntEz
¶

ntF
¶

ntFx
¶

ntFy
¶

ntFz
¶

ntN
¶

number
()¶

plotGrid
()¶

plotImage
()¶

projectEdgeVector
(eV)¶ Given a vector, eV, in cartesian coordinates, this will project it onto the mesh using the tangents
Parameters: eV (numpy.ndarray) – edge vector with shape (nE, dim) Return type: numpy.ndarray Returns: projected edge vector, (nE, )

projectFaceVector
(fV)¶ Given a vector, fV, in cartesian coordinates, this will project it onto the mesh using the normals
Parameters: fV (numpy.ndarray) – face vector with shape (nF, dim) Return type: numpy.ndarray Returns: projected face vector, (nF, )

readModelUBC
(mesh, fileName)¶ Read UBC OcTree model and get vector :param string fileName: path to the UBC GIF model file to read :rtype: numpy.ndarray :return: OcTree model

readUBC
(TreeMesh, meshFile)¶ Read UBC 3D OcTree mesh file Input: :param str meshFile: path to the UBC GIF OcTree mesh file to read :rtype: discretize.TreeMesh :return: The octree mesh

reference_is_rotated
¶ True if the axes are rotated from the traditional <X,Y,Z> system with vectors of \((1,0,0)\), \((0,1,0)\), and \((0,0,1)\)

reference_system
¶ reference_system (
String
): The type of coordinate reference frame. Can take on the values cartesian, cylindrical, or spherical. Abbreviations of these are allowed., a unicode string, Default: cartesian

refine
()¶

rotation_matrix
¶ Builds a rotation matrix to transform coordinates from their coordinate system into a conventional cartesian system. This is built off of the three axis_u, axis_v, and axis_w properties; these mapping coordinates use the letters U, V, and W (the three letters preceding X, Y, and Z in the alphabet) to define the projection of the X, Y, and Z durections. These UVW vectors describe the placement and transformation of the mesh’s coordinate sytem assuming at most 3 directions.
Why would you want to use these UVW mapping vectors the this rotation_matrix property? They allow us to define the realationship between local and global coordinate systems and provide a tool for switching between the two while still maintaing the connectivity of the mesh’s cells. For a visual example of this, please see the figure in the docs for the
vtkInterface
.

serialize
(include_class=True, save_dynamic=False, **kwargs)¶ Serializes a HasProperties instance to dictionary
This uses the Property serializers to serialize all Property values to a JSONcompatible dictionary. Properties that are undefined are not included. If the HasProperties instance contains a reference to itself, a
properties.SelfReferenceError
will be raised.Parameters:
 include_class  If True (the default), the name of the class
will also be saved to the serialized dictionary under key
'__class__'
 save_dynamic  If True, dynamic properties are written to the serialized dict (default: False).
 Any other keyword arguments will be passed through to the Property serializers.
 include_class  If True (the default), the name of the class
will also be saved to the serialized dictionary under key

tangents
¶ Edge Tangents
Return type: numpy.ndarray Returns: normals, (sum(nE), dim)

toVTK
(mesh, models=None)¶ Convert this mesh object to it’s proper
vtki
data object with the given model dictionary as the cell data of that dataset.Input:
Parameters: models (dict(numpy.ndarray)) – Name(‘s) and array(‘s). Match number of cells

validate
()¶ Call all registered class validator methods
These are all methods decorated with
@properties.validator
. Validator methods are expected to raise a ValidationError if they fail.

vectorCCx
¶ Cellcentered grid vector (1D) in the x direction.

vectorCCy
¶ Cellcentered grid vector (1D) in the y direction.

vectorCCz
¶ Cellcentered grid vector (1D) in the z direction.

vectorNx
¶ Nodal grid vector (1D) in the x direction.

vectorNy
¶ Nodal grid vector (1D) in the y direction.

vectorNz
¶ Nodal grid vector (1D) in the z direction.

vnE
¶ Total number of edges in each direction
Return type: numpy.ndarray Returns: [nEx, nEy, nEz], (dim, ) import discretize import numpy as np M = discretize.TensorMesh([np.ones(n) for n in [2,3]]) M.plotGrid(edges=True, showIt=True)
(Source code, png, hires.png, pdf)

vnF
¶ Total number of faces in each direction
Return type: numpy.ndarray Returns: [nFx, nFy, nFz], (dim, ) import discretize import numpy as np M = discretize.TensorMesh([np.ones(n) for n in [2,3]]) M.plotGrid(faces=True, showIt=True)
(Source code, png, hires.png, pdf)

vol
¶

writeUBC
(mesh, fileName, models=None)¶ Write UBC ocTree mesh and model files from a octree mesh and model. :param string fileName: File to write to :param dict models: Models in a dict, where each key is the filename

writeVTK
(mesh, fileName, models=None, directory='')¶ Makes and saves a VTK object from this mesh and given models
Input:
Parameters:

x0
¶
 axis_u (
Mesh IO¶

class
discretize.MeshIO.
TreeMeshIO
[source]¶ Bases:
object

classmethod
readUBC
(TreeMesh, meshFile)[source]¶ Read UBC 3D OcTree mesh file Input: :param str meshFile: path to the UBC GIF OcTree mesh file to read :rtype: discretize.TreeMesh :return: The octree mesh

classmethod