discretize.CurvilinearMesh¶

class
discretize.
CurvilinearMesh
(*args, **kwargs)[source]¶ Bases:
discretize.base.base_mesh.BaseRectangularMesh
,discretize.DiffOperators.DiffOperators
,discretize.InnerProducts.InnerProducts
,discretize.View.CurviView
CurvilinearMesh is a mesh class that deals with curvilinear meshes.
Example of a curvilinear mesh:
import discretize X, Y = discretize.utils.exampleLrmGrid([3,3],'rotate') mesh = discretize.CurvilinearMesh([X, Y]) mesh.plotGrid(show_it=True)
(Source code, png, pdf)
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: Xaxis_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: Yaxis_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: Znodes (a list of
Array
): List of arrays describing the node locations, a list (each item is a list or numpy array of <class ‘float’>, <class ‘int’> with shape (*, *, *) or (*, *)) with length between 2 and 3reference_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: cartesianx0 (
Array
): origin of the mesh (dim, ), a list or numpy array of <class ‘float’>, <class ‘int’> with shape (*)
 Attributes
area
Area of the faces
aveCC2F
Construct the averaging operator on cell centers to faces.
aveCCV2F
Construct the averaging operator on cell centers to faces as a vector.
aveE2CC
Construct the averaging operator on cell edges to cell centers.
aveE2CCV
Construct the averaging operator on cell edges to cell centers.
aveEx2CC
Construct the averaging operator on cell edges in the x direction to cell centers.
aveEy2CC
Construct the averaging operator on cell edges in the y direction to cell centers.
aveEz2CC
Construct the averaging operator on cell edges in the z direction to cell centers.
aveF2CC
Construct the averaging operator on cell faces to cell centers.
aveF2CCV
Construct the averaging operator on cell faces to cell centers.
aveFx2CC
Construct the averaging operator on cell faces in the x direction to cell centers.
aveFy2CC
Construct the averaging operator on cell faces in the y direction to cell centers.
aveFz2CC
Construct the averaging operator on cell faces in the z direction to cell centers.
aveN2CC
Construct the averaging operator on cell nodes to cell centers.
aveN2E
Construct the averaging operator on cell nodes to cell edges, keeping each dimension separate.
aveN2F
Construct the averaging operator on cell nodes to cell faces, keeping each dimension separate.
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: Xaxis_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: Yaxis_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: ZcellGrad
The cell centered Gradient, takes you to cell faces.
cellGradBC
The cell centered Gradient boundary condition matrix
cellGradx
Cell centered Gradient in the x dimension.
 cellGrady
cellGradz
Cell centered Gradient in the x dimension.
dim
The dimension of the mesh (1, 2, or 3).
edge
Edge lengths
edgeCurl
Construct the 3D curl operator.
faceDiv
Construct divergence operator (facestg to cellcentres).
faceDivx
Construct divergence operator in the x component (facestg to cellcentres).
 faceDivy
faceDivz
Construct divergence operator in the z component (facestg to cellcenters).
gridCC
Cellcentered grid
gridEx
Edge staggered grid in the x direction.
gridEy
Edge staggered grid in the y direction.
gridEz
Edge staggered grid in the z direction.
gridFx
Face staggered grid in the x direction.
gridFy
Face staggered grid in the y direction.
gridFz
Face staggered grid in the y direction.
gridN
Nodal grid.
nC
Total number of cells
nCx
Number of cells in the x direction
nCy
Number of cells in the y direction
nCz
Number of cells in the z direction
nE
Total number of edges.
nEx
Number of xedges
nEy
Number of yedges
nEz
Number of zedges
nF
Total number of faces.
nFx
Number of xfaces
nFy
Number of yfaces
nFz
Number of zfaces
nN
Total number of nodes
nNx
Number of nodes in the xdirection
nNy
Number of nodes in the ydirection
nNz
Number of nodes in the zdirection
nodalGrad
Construct gradient operator (nodes to edges).
nodalLaplacian
Construct laplacian operator (nodes to edges).
nodes
nodes (a list of
Array
): List of arrays describing the node locations, a list (each item is a list or numpy array of <class ‘float’>, <class ‘int’> with shape (*, *, *) or (*, *)) with length between 2 and 3normals
Face normals: calling this will average the computed normals so that there is one per face.
reference_is_rotated
True if the axes are rotated from the traditional <X,Y,Z> system
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: cartesianrotation_matrix
Builds a rotation matrix to transform coordinates from their coordinate system into a conventional cartesian system.
tangents
Edge tangents
vnC
Total number of cells in each direction
vnE
Total number of edges in each direction
vnEx
Number of xedges in each direction
vnEy
Number of yedges in each direction
vnEz
Number of zedges in each direction
vnF
Total number of faces in each direction
vnFx
Number of xfaces in each direction
vnFy
Number of yfaces in each direction
vnFz
Number of zfaces in each direction
vnN
Total number of nodes in each direction
vol
Construct cell volumes of the 3D model as 1d array
x0
x0 (
Array
): origin of the mesh (dim, ), a list or numpy array of <class ‘float’>, <class ‘int’> with shape (*)
Methods
Generic (shallow and deep) copying operations.
plotImage
Attributes¶

CurvilinearMesh.
area
¶ Area of the faces

CurvilinearMesh.
aveCC2F
¶ Construct the averaging operator on cell centers to faces.

CurvilinearMesh.
aveCCV2F
¶ Construct the averaging operator on cell centers to faces as a vector.

CurvilinearMesh.
aveE2CC
¶ Construct the averaging operator on cell edges to cell centers.

CurvilinearMesh.
aveE2CCV
¶ Construct the averaging operator on cell edges to cell centers.

CurvilinearMesh.
aveEx2CC
¶ Construct the averaging operator on cell edges in the x direction to cell centers.

CurvilinearMesh.
aveEy2CC
¶ Construct the averaging operator on cell edges in the y direction to cell centers.

CurvilinearMesh.
aveEz2CC
¶ Construct the averaging operator on cell edges in the z direction to cell centers.

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

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

CurvilinearMesh.
aveFx2CC
¶ Construct the averaging operator on cell faces in the x direction to cell centers.

CurvilinearMesh.
aveFy2CC
¶ Construct the averaging operator on cell faces in the y direction to cell centers.

CurvilinearMesh.
aveFz2CC
¶ Construct the averaging operator on cell faces in the z direction to cell centers.

CurvilinearMesh.
aveN2CC
¶ Construct the averaging operator on cell nodes to cell centers.

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

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

CurvilinearMesh.
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

CurvilinearMesh.
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

CurvilinearMesh.
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

CurvilinearMesh.
cellGrad
¶ The cell centered Gradient, takes you to cell faces.

CurvilinearMesh.
cellGradBC
¶ The cell centered Gradient boundary condition matrix

CurvilinearMesh.
cellGradx
¶ Cell centered Gradient in the x dimension. Has neumann boundary conditions.

CurvilinearMesh.
cellGrady
¶

CurvilinearMesh.
cellGradz
¶ Cell centered Gradient in the x dimension. Has neumann boundary conditions.

CurvilinearMesh.
dim
¶ The dimension of the mesh (1, 2, or 3).
 Returns
 int
dimension of the mesh

CurvilinearMesh.
edge
¶ Edge lengths

CurvilinearMesh.
edgeCurl
¶ Construct the 3D curl operator.

CurvilinearMesh.
faceDiv
¶ Construct divergence operator (facestg to cellcentres).

CurvilinearMesh.
faceDivx
¶ Construct divergence operator in the x component (facestg to cellcentres).

CurvilinearMesh.
faceDivy
¶

CurvilinearMesh.
faceDivz
¶ Construct divergence operator in the z component (facestg to cellcenters).

CurvilinearMesh.
gridCC
¶ Cellcentered grid

CurvilinearMesh.
gridEx
¶ Edge staggered grid in the x direction.

CurvilinearMesh.
gridEy
¶ Edge staggered grid in the y direction.

CurvilinearMesh.
gridEz
¶ Edge staggered grid in the z direction.

CurvilinearMesh.
gridFx
¶ Face staggered grid in the x direction.

CurvilinearMesh.
gridFy
¶ Face staggered grid in the y direction.

CurvilinearMesh.
gridFz
¶ Face staggered grid in the y direction.

CurvilinearMesh.
gridN
¶ Nodal grid.

CurvilinearMesh.
nCy
¶ Number of cells in the y direction
 Return type
 Returns
nCy or None if dim < 2

CurvilinearMesh.
nCz
¶ Number of cells in the z direction
 Return type
 Returns
nCz or None if dim < 3

CurvilinearMesh.
nE
¶ Total number of edges.
 Returns
 nEint = sum([nEx, nEy, nEz])

CurvilinearMesh.
nNy
¶ Number of nodes in the ydirection
 Return type
 Returns
nNy or None if dim < 2

CurvilinearMesh.
nNz
¶ Number of nodes in the zdirection
 Return type
 Returns
nNz or None if dim < 3

CurvilinearMesh.
nodalGrad
¶ Construct gradient operator (nodes to edges).

CurvilinearMesh.
nodalLaplacian
¶ Construct laplacian operator (nodes to edges).

CurvilinearMesh.
nodes
¶ nodes (a list of
Array
): List of arrays describing the node locations, a list (each item is a list or numpy array of <class ‘float’>, <class ‘int’> with shape (*, *, *) or (*, *)) with length between 2 and 3

CurvilinearMesh.
normals
¶ Face normals: calling this will average the computed normals so that there is one per face. This is especially relevant in 3D, as there are up to 4 different normals for each face that will be different.
To reshape the normals into a matrix and get the y component:
NyX, NyY, NyZ = M.r(M.normals, 'F', 'Fy', 'M')

CurvilinearMesh.
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 \((0,0,1)\)

CurvilinearMesh.
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

CurvilinearMesh.
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
InterfaceVTK
.

CurvilinearMesh.
tangents
¶ Edge tangents

CurvilinearMesh.
vnC
¶ Total number of cells in each direction
 Return type
 Returns
[nCx, nCy, nCz]

CurvilinearMesh.
vnE
¶ Total number of edges in each direction
 Returns
 vnEnumpy.ndarray = [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, show_it=True)
(Source code, png, pdf)

CurvilinearMesh.
vnEx
¶ Number of xedges in each direction
 Return type
 Returns
vnEx

CurvilinearMesh.
vnEy
¶ Number of yedges in each direction
 Return type
 Returns
vnEy or None if dim < 2

CurvilinearMesh.
vnEz
¶ Number of zedges in each direction
 Return type
 Returns
vnEz or None if dim < 3

CurvilinearMesh.
vnF
¶ Total number of faces in each direction
 Return type
 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, show_it=True)
(Source code, png, pdf)

CurvilinearMesh.
vnFx
¶ Number of xfaces in each direction
 Return type
 Returns
vnFx

CurvilinearMesh.
vnFy
¶ Number of yfaces in each direction
 Return type
 Returns
vnFy or None if dim < 2

CurvilinearMesh.
vnFz
¶ Number of zfaces in each direction
 Return type
 Returns
vnFz or None if dim < 3

CurvilinearMesh.
vnN
¶ Total number of nodes in each direction
 Return type
 Returns
[nNx, nNy, nNz]

CurvilinearMesh.
vol
¶ Construct cell volumes of the 3D model as 1d array
Methods¶

CurvilinearMesh.
copy
()¶ Make a copy of the current mesh

classmethod
CurvilinearMesh.
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.

CurvilinearMesh.
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
.

static
CurvilinearMesh.
from_omf
(element)¶ Convert an OMF element to it’s proper
discretize
type. Automatically determines the output type. Returns both the mesh and a dictionary of model arrays.

CurvilinearMesh.
getBCProjWF
(BC, discretization='CC')¶ The weak form boundary condition projection matrices.
Examples
# Neumann in all directions BC = 'neumann' # 3D, Dirichlet in y Neumann else BC = ['neumann', 'dirichlet', 'neumann'] # 3D, Neumann in x on bottom of domain, Dirichlet else BC = [['neumann', 'dirichlet'], 'dirichlet', 'dirichlet']

CurvilinearMesh.
getBCProjWF_simple
(discretization='CC')¶ The weak form boundary condition projection matrices when mixed boundary condition is used

CurvilinearMesh.
getEdgeInnerProduct
(prop=None, invProp=False, invMat=False, doFast=True)¶ Generate the edge inner product matrix
 Parameters
 propnumpy.ndarray
material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 invPropbool
inverts the material property
 invMatbool
inverts the matrix
 doFastbool
do a faster implementation if available.
 Returns
 scipy.sparse.csr_matrix
M, the inner product matrix (nE, nE)

CurvilinearMesh.
getEdgeInnerProductDeriv
(prop, doFast=True, invProp=False, invMat=False)¶  Parameters
 propnumpy.ndarray
material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 doFastbool
do a faster implementation if available.
 invPropbool
inverts the material property
 invMatbool
inverts the matrix
 Returns
 scipy.sparse.csr_matrix
dMdm, the derivative of the inner product matrix (nE, nC*nA)

CurvilinearMesh.
getFaceInnerProduct
(prop=None, invProp=False, invMat=False, doFast=True)¶ Generate the face inner product matrix
 Parameters
 propnumpy.ndarray
material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 invPropbool
inverts the material property
 invMatbool
inverts the matrix
 doFastbool
do a faster implementation if available.
 Returns
 scipy.sparse.csr_matrix
M, the inner product matrix (nF, nF)

CurvilinearMesh.
getFaceInnerProductDeriv
(prop, doFast=True, invProp=False, invMat=False)¶  Parameters
 propnumpy.ndarray
material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
 doFast :
bool do a faster implementation if available.
 invPropbool
inverts the material property
 invMatbool
inverts the matrix
 Returns
 scipy.sparse.csr_matrix
dMdmu(u), the derivative of the inner product matrix for a certain u

CurvilinearMesh.
plotGrid
(ax=None, nodes=False, faces=False, centers=False, edges=False, lines=True, show_it=False, **kwargs)¶ Plot the nodal, cellcentered and staggered grids for 1, 2 and 3 dimensions.
import discretize X, Y = discretize.utils.exampleLrmGrid([3, 3], 'rotate') M = discretize.CurvilinearMesh([X, Y]) M.plotGrid(show_it=True)
(Source code, png, pdf)

CurvilinearMesh.
plotImage
(v, v_type='CC', grid=False, view='real', ax=None, clim=None, show_it=False, pcolor_opts=None, grid_opts=None, range_x=None, range_y=None, **kwargs)¶

CurvilinearMesh.
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
 Returns
projected edge vector, (nE, )

CurvilinearMesh.
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
 Returns
projected face vector, (nF, )

CurvilinearMesh.
r
(x, xType='CC', outType='CC', format='V')¶ r is a quick reshape command that will do the best it can at giving you what you want.
For example, you have a face variable, and you want the x component of it reshaped to a 3D matrix.
r can fulfil your dreams:
mesh.r(V, 'F', 'Fx', 'M')        {    How: 'M' or ['V'] for a matrix    (ndgrid style) or a vector (n x dim)    }   {   What you want: ['CC'], 'N',   'F', 'Fx', 'Fy', 'Fz',   'E', 'Ex', 'Ey', or 'Ez'   }  {  What is it: ['CC'], 'N',  'F', 'Fx', 'Fy', 'Fz',  'E', 'Ex', 'Ey', or 'Ez'  } { The input: as a list or ndarray }
For example:
# Separates each component of the Ex grid into 3 matrices Xex, Yex, Zex = r(mesh.gridEx, 'Ex', 'Ex', 'M') # Given an edge vector, return just the x edges as a vector XedgeVector = r(edgeVector, 'E', 'Ex', 'V') # Separates each component of the edgeVector into 3 vectors eX, eY, eZ = r(edgeVector, 'E', 'E', 'V')

CurvilinearMesh.
save
(filename='mesh.json', verbose=False)¶ Save the mesh to json :param str file: filename for saving the casing properties :param str directory: working directory for saving the file

CurvilinearMesh.
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.

CurvilinearMesh.
setCellGradBC
(BC)¶ Function that sets the boundary conditions for cellcentred derivative operators.
Examples
..code:: python
# Neumann in all directions BC = ‘neumann’
# 3D, Dirichlet in y Neumann else BC = [‘neumann’, ‘dirichlet’, ‘neumann’]
# 3D, Neumann in x on bottom of domain, Dirichlet else BC = [[‘neumann’, ‘dirichlet’], ‘dirichlet’, ‘dirichlet’]

CurvilinearMesh.
toVTK
(models=None)¶ Convert this mesh object to it’s proper VTK or
pyvista
data object with the given model dictionary as the cell data of that dataset. Parameters
 modelsdict(numpy.ndarray)
Name(‘s) and array(‘s). Match number of cells

CurvilinearMesh.
to_omf
(models=None)¶ Convert this mesh object to it’s proper
omf
data object with the given model dictionary as the cell data of that dataset. Parameters
 modelsdict(numpy.ndarray)
Name(‘s) and array(‘s). Match number of cells

CurvilinearMesh.
to_vtk
(models=None)¶ Convert this mesh object to it’s proper VTK or
pyvista
data object with the given model dictionary as the cell data of that dataset. Parameters
 modelsdict(numpy.ndarray)
Name(‘s) and array(‘s). Match number of cells

CurvilinearMesh.
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.

CurvilinearMesh.
writeVTK
(filename, models=None, directory='')¶ Makes and saves a VTK object from this mesh and given models
 Parameters
 filenamestr
path to the output vtk file or just its name if directory is specified
 modelsdict
dictionary of numpy.array  Name(‘s) and array(‘s). Match number of cells
 directorystr
directory where the UBC GIF file lives

CurvilinearMesh.
write_vtk
(filename, models=None, directory='')¶ Makes and saves a VTK object from this mesh and given models
 Parameters
 filenamestr
path to the output vtk file or just its name if directory is specified
 modelsdict
dictionary of numpy.array  Name(‘s) and array(‘s). Match number of cells
 directorystr
directory where the UBC GIF file lives