Merge branch 'master' of https://bitbucket.org/rcockett/simpeg

code/BaseMesh.py

@@ -0,0 +1,205 @@
+import numpy as np
+
+
+class BaseMesh(object):
+    """BaseMesh does all the counting you don't want to do.
+
+    x0          origin                    ndarray   (dim, )
+    n           number of cells           ndarray   (dim, )
+    dim         dimension of mesh         int       1, 2, or 3
+
+    nCx         num cells in x dir        int
+    nCy         num cells in y dir        int
+    nCz         num cells in z dir        int
+    nC          total number of cells     int
+
+    nNx         num nodes in x dir        int
+    nNy         num nodes in y dir        int
+    nNz         num nodes in z dir        int
+    nN          total number of nodes     int
+
+    nEx         num edges in x dir        ndarray   [nEx_x, nEx_y, nEx_z]
+    nEy         num edges in y dir        ndarray   [nEy_x, nEy_y, nEy_z]
+    nEz         num edges in z dir        ndarray   [nEz_x, nEz_y, nEz_z]
+    nE          total number of edges     ndarray   (dim, )
+
+    nFx         num faces in x dir        ndarray   [nFx_x, nFx_y, nFx_z]
+    nFy         num faces in y dir        ndarray   [nFy_x, nFy_y, nFy_z]
+    nFz         num faces in z dir        ndarray   [nFz_x, nFz_y, nFz_z]
+    nF          total number of faces     ndarray   (dim, )
+
+    """
+    def __init__(self, n, x0=None):
+
+        # Check inputs
+        if x0 is None:
+            x0 = np.zeros(len(n))
+
+        if not len(n) == len(x0):
+            raise Exception("Dimension mismatch. x0 != len(n)")
+
+        if len(n) > 3:
+            raise Exception("Dimensions higher than 3 are not supported.")
+
+        # Ensure x0 & n are 1D vectors
+        self._n = np.array(n, dtype=int).ravel()
+        self._x0 = np.array(x0).ravel()
+        self._dim = len(n)
+
+    def x0():
+        doc = "Origin of the mesh"
+        fget = lambda self: self._x0
+        return locals()
+    x0 = property(**x0())
+
+    def n():
+        doc = "Number of Cells in each dimension (array of integers)"
+        fget = lambda self: self._n
+        return locals()
+    n = property(**n())
+
+    def dim():
+        doc = "The dimension of the mesh (1, 2, or 3)."
+        fget = lambda self: self._dim
+        return locals()
+    dim = property(**dim())
+
+    def nCx():
+        doc = "Number oc cells in the x direction"
+        fget = lambda self: self.n[0]
+        return locals()
+    nCx = property(**nCx())
+
+    def nCy():
+        doc = "Number of cells in the y direction"
+
+        def fget(self):
+            if self.dim > 1:
+                return self.n[1]
+            else:
+                return None
+        return locals()
+    nCy = property(**nCy())
+
+    def nCz():
+        doc = "Number of cells in the z direction"
+
+        def fget(self):
+            if self.dim > 2:
+                return self.n[2]
+            else:
+                return None
+        return locals()
+    nCz = property(**nCz())
+
+    def nC():
+        doc = "Total number of cells"
+        fget = lambda self: np.prod(self.n)
+        return locals()
+    nC = property(**nC())
+
+    def nNx():
+        doc = "Number of nodes in the x-direction"
+        fget = lambda self: self.nCx + 1
+        return locals()
+    nNx = property(**nNx())
+
+    def nNy():
+        doc = "Number of noes in the y-direction"
+
+        def fget(self):
+            if self.dim > 1:
+                return self.n[1] + 1
+            else:
+                return None
+        return locals()
+    nNy = property(**nNy())
+
+    def nNz():
+        doc = "Number of nodes in the z-direction"
+
+        def fget(self):
+            if self.dim > 2:
+                return self.n[2] + 1
+            else:
+                return None
+        return locals()
+    nNz = property(**nNz())
+
+    def nN():
+        doc = "Total number of nodes"
+        fget = lambda self: self.n + 1
+        return locals()
+    nN = property(**nN())
+
+    def nEx():
+        doc = "Number of x-edges"
+        fget = lambda self: np.array([x for x in [self.nCx, self.nNy, self.nNz] if not x is None])
+        return locals()
+    nEx = property(**nEx())
+
+    def nEy():
+        doc = "Number of y-edges"
+
+        def fget(self):
+            if self.dim > 1:
+                return np.array([x for x in [self.nNx, self.nCy, self.nNz] if not x is None])
+            else:
+                return None
+        return locals()
+    nEy = property(**nEy())
+
+    def nEz():
+        doc = "Number of z-edges"
+
+        def fget(self):
+            if self.dim > 2:
+                return np.array([x for x in [self.nNx, self.nNy, self.nCz] if not x is None])
+            else:
+                return None
+        return locals()
+    nEz = property(**nEz())
+
+    def nE():
+        doc = "Total number of edges"
+        fget = lambda self: np.array([np.prod(x) for x in [self.nEx, self.nEy, self.nEz] if not x is None])
+        return locals()
+    nE = property(**nE())
+
+    def nFx():
+        doc = "Number of x-faces"
+        fget = lambda self: np.array([x for x in [self.nNx, self.nCy, self.nCz] if not x is None])
+        return locals()
+    nFx = property(**nFx())
+
+    def nFy():
+        doc = "Number of y-faces"
+
+        def fget(self):
+            if self.dim > 1:
+                return np.array([x for x in [self.nCx, self.nNy, self.nCz] if not x is None])
+            else:
+                return None
+        return locals()
+    nFy = property(**nFy())
+
+    def nFz():
+        doc = "Number of z-faces"
+
+        def fget(self):
+            if self.dim > 2:
+                return np.array([x for x in [self.nCx, self.nCy, self.nNz] if not x is None])
+            else:
+                return None
+        return locals()
+    nFz = property(**nFz())
+
+    def nF():
+        doc = "Total number of faces in each dimension"
+        fget = lambda self: np.array([np.prod(x) for x in [self.nFx, self.nFy, self.nFz] if not x is None])
+        return locals()
+    nF = property(**nF())
+
+if __name__ == '__main__':
+    m = BaseMesh([3, 2, 4])
+    print m.n

code/Mesh.py

@@ -1,130 +0,0 @@
-import numpy as np
-
-
-class Mesh(object):
-    """docstring for Mesh"""
-    def __init__(self, h):
-
-        if type(h) != list:
-            raise Exception("Type of h must be a list variable. e.g. [5, 4, 2] or [[1,1,1],[0.5,0.5]]")
-
-        if np.sum([np.size(x) for x in h]) == len(h):
-            # We have specified a shorthand for the mesh e.g. [5, 4, 2]
-            # We will recreate the h, such that it lies on the unit cube/square/line
-            domain = 1.  # (must be a float)
-            h = [np.ones(x)*(domain/x) for x in h]
-
-        dim = len(h)
-
-        if dim > 1 and np.all([len(np.shape(x)) > 1 and np.shape(x)[1] > 1 for x in h]):
-            # The h has internal structure, and is not a vector
-            # Thus, we must be describing the verticies of the mesh
-            # Hence, the mesh is a Logically Orthogonal Mesh
-            self.meshType = 'LOM'
-        else:
-            # Could add other checks, but here the default is a rectangular mesh
-            self.meshType = 'RECT'
-
-        if self.meshType != 'LOM':
-            # Ensure that the h is a numpy array, with shape: (n,)
-            h = [np.array(x).ravel() for x in h]
-
-        # Define the number of nodes
-        if self.meshType == 'LOM':
-            self._nnodes = np.array(np.shape(h[0]))
-        else:
-            self._nnodes = np.array([len(x) for x in h]) + 1
-
-        self._nc = self._nnodes - 1
-        self._ncells = np.prod(self._nc)
-        self._h = h
-        self._dim = dim
-
-        m = self._nnodes
-        if dim == 1:
-            self._nfaces = np.prod(m)
-            self._nedges = np.prod(m)
-        elif dim == 2:
-            self._nfx = m - [0, 1]
-            self._nfy = m - [1, 0]
-            self._nex = m - [1, 0]
-            self._ney = m - [0, 1]
-
-            self._nfaces = [np.prod(self.nfx), np.prod(self.nfy)]
-            self._nedges = [np.prod(self.nex), np.prod(self.ney)]
-        elif dim == 3:
-            self._nfx = m - [0, 1, 1]
-            self._nfy = m - [1, 0, 1]
-            self._nfz = m - [1, 1, 0]
-            self._nex = m - [1, 0, 0]
-            self._ney = m - [0, 1, 0]
-            self._nez = m - [0, 0, 1]
-
-            self._nfaces = [np.prod(self.nfx), np.prod(self.nfy), np.prod(self.nfz)]
-            self._nedges = [np.prod(self.nex), np.prod(self.ney), np.prod(self.nez)]
-
-    def dim():
-        doc = "The dimension of the mesh: 1, 2, or 3"
-        fget = lambda self: self._dim
-        return locals()
-    dim = property(**dim())
-
-    def nc():
-        doc = "Number of cells in each direction of the mesh"
-        fget = lambda self: self._nc
-        return locals()
-    nc = property(**nc())
-
-    def ncells():
-        doc = "Number of cells in the mesh"
-        fget = lambda self: self._ncells
-        return locals()
-    ncells = property(**ncells())
-
-    def nfaces():
-        doc = "Number of faces in each direction of the mesh"
-        fget = lambda self: self._nfaces
-        return locals()
-    nfaces = property(**nfaces())
-
-    def nedges():
-        doc = "Number of edges in each direction of the mesh"
-        fget = lambda self: self._nedges
-        return locals()
-    nedges = property(**nedges())
-
-    def nfx():
-        doc = "Number of faces in the x direction of the mesh"
-        fget = lambda self: self._nfx if self.dim > 1 else None
-        return locals()
-    nfx = property(**nfx())
-
-    def nfy():
-        doc = "Number of faces in the y direction of the mesh"
-        fget = lambda self: self._nfy if self.dim > 1 else None
-        return locals()
-    nfy = property(**nfy())
-
-    def nfz():
-        doc = "Number of faces in the z direction of the mesh"
-        fget = lambda self: self._nfz if self.dim > 2 else None
-        return locals()
-    nfz = property(**nfz())
-
-    def nex():
-        doc = "Number of edges in the x direction of the mesh"
-        fget = lambda self: self._nex if self.dim > 1 else None
-        return locals()
-    nex = property(**nex())
-
-    def ney():
-        doc = "Number of edges in the y direction of the mesh"
-        fget = lambda self: self._ney if self.dim > 1 else None
-        return locals()
-    ney = property(**ney())
-
-    def nez():
-        doc = "Number of edges in the z direction of the mesh"
-        fget = lambda self: self._nez if self.dim > 2 else None
-        return locals()
-    nez = property(**nez())

code/TensorGrid.py

@@ -0,0 +1,144 @@
+import numpy as np
+from utils import ndgrid
+
+
+class TensorGrid(object):
+    """
+    Define nodal, cell-centered and staggered tensor grids for 1, 2 and 3
+    dimensions.
+
+    This class is inherited by TensorMesh
+    """
+    def __init__(self):
+        pass
+
+    def vectorNx():
+        doc = "Nodal grid vector (1D) in the x direction."
+        fget = lambda self: np.r_[0., self.hx.cumsum()] + self.x0[0]
+        return locals()
+    vectorNx = property(**vectorNx())
+
+    def vectorNy():
+        doc = "Nodal grid vector (1D) in the y direction."
+        fget = lambda self: None if self.dim < 2 else np.r_[0., self.hy.cumsum()] + self.x0[1]
+        return locals()
+    vectorNy = property(**vectorNy())
+
+    def vectorNz():
+        doc = "Nodal grid vector (1D) in the z direction."
+        fget = lambda self: None if self.dim < 3 else np.r_[0., self.hz.cumsum()] + self.x0[2]
+        return locals()
+    vectorNz = property(**vectorNz())
+
+    def vectorCCx():
+        doc = "Cell-centered grid vector (1D) in the x direction."
+        fget = lambda self: np.r_[0, self.hx[:-1].cumsum()] + self.hx*0.5 + self.x0[0]
+        return locals()
+    vectorCCx = property(**vectorCCx())
+
+    def vectorCCy():
+        doc = "Cell-centered grid vector (1D) in the y direction."
+        fget = lambda self: None if self.dim < 2 else np.r_[0, self.hy[:-1].cumsum()] + self.hy*0.5 + self.x0[1]
+        return locals()
+    vectorCCy = property(**vectorCCy())
+
+    def vectorCCz():
+        doc = "Cell-centered grid vector (1D) in the z direction."
+        fget = lambda self: None if self.dim < 3 else np.r_[0, self.hz[:-1].cumsum()] + self.hz*0.5 + self.x0[2]
+        return locals()
+    vectorCCz = property(**vectorCCz())
+
+    def gridCC():
+        doc = "Cell-centered grid."
+
+        def fget(self):
+            if self._gridCC is None:
+                self._gridCC = ndgrid([x for x in [self.vectorCCx, self.vectorCCy, self.vectorCCz] if not x is None])
+            return self._gridCC
+        return locals()
+    _gridCC = None  # Store grid by default
+    gridCC = property(**gridCC())
+
+    def gridN():
+        doc = "Nodal grid."
+
+        def fget(self):
+            if self._gridN is None:
+                self._gridN = ndgrid([x for x in [self.vectorNx, self.vectorNy, self.vectorNz] if not x is None])
+            return self._gridN
+        return locals()
+    _gridN = None  # Store grid by default
+    gridN = property(**gridN())
+
+    def gridFx():
+        doc = "Face staggered grid in the x direction."
+
+        def fget(self):
+            if self._gridFx is None:
+                self._gridFx = ndgrid([x for x in [self.vectorNx, self.vectorCCy, self.vectorCCz] if not x is None])
+            return self._gridFx
+        return locals()
+    _gridFx = None  # Store grid by default
+    gridFx = property(**gridFx())
+
+    def gridFy():
+        doc = "Face staggered grid in the y direction."
+
+        def fget(self):
+            if self._gridFy is None:
+                self._gridFy = ndgrid([x for x in [self.vectorCCx, self.vectorNy, self.vectorCCz] if not x is None])
+            return self._gridFy
+        return locals()
+    _gridFy = None  # Store grid by default
+    gridFy = property(**gridFy())
+
+    def gridFz():
+        doc = "Face staggered grid in the z direction."
+
+        def fget(self):
+            if self._gridFz is None:
+                self._gridFz = ndgrid([x for x in [self.vectorCCx, self.vectorCCy, self.vectorNz] if not x is None])
+            return self._gridFz
+        return locals()
+    _gridFz = None  # Store grid by default
+    gridFz = property(**gridFz())
+
+    def gridEx():
+        doc = "Edge staggered grid in the x direction."
+
+        def fget(self):
+            if self._gridEx is None:
+                self._gridEx = ndgrid([x for x in [self.vectorCCx, self.vectorNy, self.vectorNz] if not x is None])
+            return self._gridEx
+        return locals()
+    _gridEx = None  # Store grid by default
+    gridEx = property(**gridEx())
+
+    def gridEy():
+        doc = "Edge staggered grid in the y direction."
+
+        def fget(self):
+            if self._gridEy is None:
+                self._gridEy = ndgrid([x for x in [self.vectorNx, self.vectorCCy, self.vectorNz] if not x is None])
+            return self._gridEy
+        return locals()
+    _gridEy = None  # Store grid by default
+    gridEy = property(**gridEy())
+
+    def gridEz():
+        doc = "Edge staggered grid in the z direction."
+
+        def fget(self):
+            if self._gridEz is None:
+                self._gridEz = ndgrid([x for x in [self.vectorNx, self.vectorNy, self.vectorCCz] if not x is None])
+            return self._gridEz
+        return locals()
+    _gridEz = None  # Store grid by default
+    gridEz = property(**gridEz())
+
+    def getBoundaryIndex(self, gridType):
+        """Needed for faces edges and cells"""
+        pass
+
+    def getCellNumbering(self):
+        pass

code/TensorMesh.py

@@ -0,0 +1,82 @@
+import numpy as np
+from BaseMesh import BaseMesh
+from TensorGrid import TensorGrid
+from TensorView import TensorView
+
+
+class TensorMesh(BaseMesh, TensorGrid, TensorView):
+    """
+    TensorMesh is a mesh class that deals with tensor product meshes.
+
+    Any Mesh that has a constant width along the entire axis
+    such that it can defined by a single width vector, called 'h'.
+
+    e.g.
+
+        hx = np.array([1,1,1])
+        hy = np.array([1,2])
+        hz = np.array([1,1,1,1])
+
+        mesh = TensorMesh([hx, hy, hz])
+
+    """
+    def __init__(self, h, x0=None):
+        super(TensorMesh, self).__init__(np.array([len(x) for x in h]), x0)
+
+        assert len(h) == len(x0), "Dimension mismatch. x0 != len(h)"
+
+        for i, h_i in enumerate(h):
+            assert type(h_i) == np.ndarray, ("h[%i] is not a numpy array." % i)
+
+        # Ensure h contains 1D vectors
+        self._h = [x.ravel() for x in h]
+
+    def h():
+        doc = "h is a list containing the cell widths of the tensor mesh in each dimension."
+        fget = lambda self: self._h
+        return locals()
+    h = property(**h())
+
+    def hx():
+        doc = "Width of cells in the x direction"
+        fget = lambda self: self._h[0]
+        return locals()
+    hx = property(**hx())
+
+    def hy():
+        doc = "Width of cells in the y direction"
+        fget = lambda self: None if self.dim < 2 else self._h[1]
+        return locals()
+    hy = property(**hy())
+
+    def hz():
+        doc = "Width of cells in the z direction"
+        fget = lambda self: None if self.dim < 3 else self._h[2]
+        return locals()
+    hz = property(**hz())
+
+
+if __name__ == '__main__':
+    print('Welcome to tensor mesh!')
+
+    testDim = 1
+    h1 = 0.3*np.ones((1, 7))
+    h1[:, 0] = 0.5
+    h1[:, -1] = 0.6
+    h2 = .5 * np.ones((1, 4))
+    h3 = .4 * np.ones((1, 6))
+    x0 = np.zeros((3, 1))
+
+    if testDim == 1:
+        h = [h1]
+        x0 = x0[0]
+    elif testDim == 2:
+        h = [h1, h2]
+        x0 = x0[0:2]
+    else:
+        h = [h1, h2, h3]
+
+    I = np.linspace(0, 1, 8)
+    M = TensorMesh(h, x0)
+
+    xn = M.plotGrid()

code/TensorView.py

@@ -0,0 +1,96 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+
+
+class TensorView(object):
+    """
+    Provides viewing functions for TensorMesh
+
+    This class is inherited by TensorMesh
+    """
+    def __init__(self):
+        pass
+
+    def plotImage(self, I):
+
+        if self.dim == 1:
+            fig = plt.figure(1)
+            fig.clf()
+            ax = plt.subplot(111)
+            if np.size(I) == self.n[0]:
+                print 'cell-centered image'
+                xx = self.gridCC
+                ax.plot(xx[0], I, 'ro')
+            elif np.size(I) == self.n[0]+1:
+                print 'nodal image'
+                xx = self.gridN
+                ax.plot(xx[0], I, 'bs')
+
+            fig.show()
+
+    def plotGrid(self):
+        """Plot the nodal, cell-centered and staggered grids for 1,2 and 3 dimensions."""
+        if self.dim == 1:
+            fig = plt.figure(1)
+            fig.clf()
+            ax = plt.subplot(111)
+            xn = self.gridN
+            xc = self.gridCC
+            print xn
+            ax.hold(True)
+            ax.plot(xn, np.ones(np.shape(xn)), 'bs')
+            ax.plot(xc, np.ones(np.shape(xc)), 'ro')
+            ax.plot(xn, np.ones(np.shape(xn)), 'k--')
+            ax.grid(True)
+            ax.hold(False)
+            ax.set_xlabel('x1')
+            fig.show()
+        elif self.dim == 2:
+            fig = plt.figure(2)
+            fig.clf()
+            ax = plt.subplot(111)
+            xn = self.gridN
+            xc = self.gridCC
+            xs1 = self.gridFx
+            xs2 = self.gridFy
+
+            ax.hold(True)
+            ax.plot(xn[:, 0], xn[:, 1], 'bs')
+            ax.plot(xc[:, 0], xc[:, 1], 'ro')
+            ax.plot(xs1[:, 0], xs1[:, 1], 'g>')
+            ax.plot(xs2[:, 0], xs2[:, 1], 'g^')
+            ax.grid(True)
+            ax.hold(False)
+            ax.set_xlabel('x1')
+            ax.set_ylabel('x2')
+            fig.show()
+        elif self.dim == 3:
+            fig = plt.figure(3)
+            fig.clf()
+            ax = fig.add_subplot(111, projection='3d')
+            xn = self.gridN
+            xc = self.gridCC
+            xfs1 = self.gridFx
+            xfs2 = self.gridFy
+            xfs3 = self.gridFz
+
+            xes1 = self.gridEx
+            xes2 = self.gridEy
+            xes3 = self.gridEz
+
+            ax.hold(True)
+            ax.plot(xn[:, 0], xn[:, 1], 'bs', zs=xn[:, 2])
+            ax.plot(xc[:, 0], xc[:, 1], 'ro', zs=xc[:, 2])
+            ax.plot(xfs1[:, 0], xfs1[:, 1], 'g>', zs=xfs1[:, 2])
+            ax.plot(xfs2[:, 0], xfs2[:, 1], 'g<', zs=xfs2[:, 2])
+            ax.plot(xfs3[:, 0], xfs3[:, 1], 'g^', zs=xfs3[:, 2])
+            ax.plot(xes1[:, 0], xes1[:, 1], 'k>', zs=xes1[:, 2])
+            ax.plot(xes2[:, 0], xes2[:, 1], 'k<', zs=xes2[:, 2])
+            ax.plot(xes3[:, 0], xes3[:, 1], 'k^', zs=xes3[:, 2])
+            ax.grid(True)
+            ax.hold(False)
+            ax.set_xlabel('x1')
+            ax.set_ylabel('x2')
+            ax.set_zlabel('x3')
+            fig.show()

code/tests/__init__.py

@@ -1,3 +0,0 @@
-# init.py
-
-from test_mesh import *

code/tests/runTests.py

@@ -0,0 +1,11 @@
+import glob
+import unittest
+
+# This code will run all tests in directory named test_*.py
+
+test_file_strings = glob.glob('test_*.py')
+module_strings = [str[0:len(str)-3] for str in test_file_strings]
+suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str
+          in module_strings]
+testSuite = unittest.TestSuite(suites)
+text_runner = unittest.TextTestRunner().run(testSuite)

code/tests/runTests.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+
+python -m unittest discover

code/tests/test_basemesh.py

@@ -0,0 +1,88 @@
+import unittest
+import sys
+sys.path.append('../')
+from BaseMesh import BaseMesh
+import numpy as np
+
+
+class TestBaseMesh(unittest.TestCase):
+
+    def setUp(self):
+        self.mesh = BaseMesh([6, 2, 3])
+
+    def test_meshDimensions(self):
+        self.assertTrue(self.mesh.dim, 3)
+
+    def test_mesh_nc(self):
+        self.assertTrue(np.all(self.mesh.n == [6, 2, 3]))
+
+    def test_mesh_nc_xyz(self):
+        x = np.all(self.mesh.nCx == 6)
+        y = np.all(self.mesh.nCy == 2)
+        z = np.all(self.mesh.nCz == 3)
+
+        self.assertTrue(np.all([x, y, z]))
+
+    def test_mesh_nf(self):
+        x = np.all(self.mesh.nFx == [7, 2, 3])
+        y = np.all(self.mesh.nFy == [6, 3, 3])
+        z = np.all(self.mesh.nFz == [6, 2, 4])
+
+        self.assertTrue(np.all([x, y, z]))
+
+    def test_mesh_ne(self):
+        x = np.all(self.mesh.nEx == [6, 3, 4])
+        y = np.all(self.mesh.nEy == [7, 2, 4])
+        z = np.all(self.mesh.nEz == [7, 3, 3])
+
+        self.assertTrue(np.all([x, y, z]))
+
+    def test_mesh_numbers(self):
+        c = self.mesh.nC == 36
+        f = np.all(self.mesh.nF == [42, 54, 48])
+        e = np.all(self.mesh.nE == [72, 56, 63])
+
+        self.assertTrue(np.all([c, f, e]))
+
+
+class TestMeshNumbers2D(unittest.TestCase):
+
+    def setUp(self):
+        self.mesh = BaseMesh([6, 2])
+
+    def test_meshDimensions(self):
+        self.assertTrue(self.mesh.dim, 2)
+
+    def test_mesh_nc(self):
+        self.assertTrue(np.all(self.mesh.n == [6, 2]))
+
+    def test_mesh_nc_xyz(self):
+        x = np.all(self.mesh.nCx == 6)
+        y = np.all(self.mesh.nCy == 2)
+        z = self.mesh.nCz is None
+
+        self.assertTrue(np.all([x, y, z]))
+
+    def test_mesh_nf(self):
+        x = np.all(self.mesh.nFx == [7, 2])
+        y = np.all(self.mesh.nFy == [6, 3])
+        z = self.mesh.nFz is None
+
+        self.assertTrue(np.all([x, y, z]))
+
+    def test_mesh_ne(self):
+        x = np.all(self.mesh.nEx == [6, 3])
+        y = np.all(self.mesh.nEy == [7, 2])
+        z = self.mesh.nEz is None
+
+        self.assertTrue(np.all([x, y, z]))
+
+    def test_mesh_numbers(self):
+        c = self.mesh.nC == 12
+        f = np.all(self.mesh.nF == [14, 18])
+        e = np.all(self.mesh.nE == [18, 14])
+
+        self.assertTrue(np.all([c, f, e]))
+
+if __name__ == '__main__':
+    unittest.main()

code/tests/test_mesh.py

@@ -1,74 +0,0 @@
-import unittest
-import sys
-sys.path.append('../')
-from Mesh import Mesh
-import numpy as np
-
-
-class TestMeshNumbers3D(unittest.TestCase):
-
-    def setUp(self):
-        self.mesh = Mesh([6, 2, 3])
-
-    def test_meshDimensions(self):
-        self.assertTrue(self.mesh.dim, 3)
-
-    def test_mesh_nc(self):
-        self.assertTrue(np.all(self.mesh.nc == [6, 2, 3]))
-
-    def test_mesh_nf(self):
-        x = np.all(self.mesh.nfx == [7, 2, 3])
-        y = np.all(self.mesh.nfy == [6, 3, 3])
-        z = np.all(self.mesh.nfz == [6, 2, 4])
-
-        self.assertTrue(np.all([x, y, z]))
-
-    def test_mesh_ne(self):
-        x = np.all(self.mesh.nex == [6, 3, 4])
-        y = np.all(self.mesh.ney == [7, 2, 4])
-        z = np.all(self.mesh.nez == [7, 3, 3])
-
-        self.assertTrue(np.all([x, y, z]))
-
-    def test_mesh_numbers(self):
-        c = self.mesh.ncells == 36
-        f = np.all(self.mesh.nfaces == [42, 54, 48])
-        e = np.all(self.mesh.nedges == [72, 56, 63])
-
-        self.assertTrue(np.all([c, f, e]))
-
-
-class TestMeshNumbers2D(unittest.TestCase):
-
-    def setUp(self):
-        self.mesh = Mesh([6, 2])
-
-    def test_meshDimensions(self):
-        self.assertTrue(self.mesh.dim, 2)
-
-    def test_mesh_nc(self):
-        self.assertTrue(np.all(self.mesh.nc == [6, 2]))
-
-    def test_mesh_nf(self):
-        x = np.all(self.mesh.nfx == [7, 2])
-        y = np.all(self.mesh.nfy == [6, 3])
-        z = self.mesh.nfz is None
-
-        self.assertTrue(np.all([x, y, z]))
-
-    def test_mesh_ne(self):
-        x = np.all(self.mesh.nex == [6, 3])
-        y = np.all(self.mesh.ney == [7, 2])
-        z = self.mesh.nez is None
-
-        self.assertTrue(np.all([x, y, z]))
-
-    def test_mesh_numbers(self):
-        c = self.mesh.ncells == 12
-        f = np.all(self.mesh.nfaces == [14, 18])
-        e = np.all(self.mesh.nedges == [18, 14])
-
-        self.assertTrue(np.all([c, f, e]))
-
-if __name__ == '__main__':
-    unittest.main()

code/tests/test_tensorMesh.py

@@ -0,0 +1,34 @@
+import numpy as np
+import unittest
+import sys
+sys.path.append('../')
+from TensorMesh import TensorMesh
+
+
+class TestSequenceFunctions(unittest.TestCase):
+
+    def setUp(self):
+        a = np.array([1, 1, 1])
+        b = np.array([1, 2])
+        x0 = np.array([3, 5])
+        self.mesh2 = TensorMesh([a, b], x0)
+
+    def test_vectorN_2D(self):
+        testNx = np.array([3, 4, 5, 6])
+        testNy = np.array([5, 6, 8])
+
+        xtest = np.all(self.mesh2.vectorNx == testNx)
+        ytest = np.all(self.mesh2.vectorNy == testNy)
+        self.assertTrue(xtest and ytest)
+
+    def test_vectorCC_2D(self):
+        testNx = np.array([3.5, 4.5, 5.5])
+        testNy = np.array([5.5, 7])
+
+        xtest = np.all(self.mesh2.vectorCCx == testNx)
+        ytest = np.all(self.mesh2.vectorCCy == testNy)
+        self.assertTrue(xtest and ytest)
+
+
+if __name__ == '__main__':
+    unittest.main()

code/tests/test_utils.py

@@ -0,0 +1,53 @@
+import numpy as np
+import unittest
+import sys
+sys.path.append('../')
+from utils import mkvc, ndgrid
+
+
+class TestSequenceFunctions(unittest.TestCase):
+
+    def setUp(self):
+        self.a = np.array([1, 2, 3])
+        self.b = np.array([1, 2])
+        self.c = np.array([1, 2, 3, 4])
+
+    def test_mkvc1(self):
+        x = mkvc(self.a)
+        self.assertTrue(x.shape, (3,))
+
+    def test_mkvc2(self):
+        x = mkvc(self.a, 2)
+        self.assertTrue(x.shape, (3, 1))
+
+    def test_mkvc3(self):
+        x = mkvc(self.a, 3)
+        self.assertTrue(x.shape, (3, 1, 1))
+
+    def test_ndgrid_2D(self):
+        XY = ndgrid([self.a, self.b])
+
+        X1_test = np.array([1, 2, 3, 1, 2, 3])
+        X2_test = np.array([1, 1, 1, 2, 2, 2])
+
+        xtest = np.all(XY[:, 0] == X1_test)
+        ytest = np.all(XY[:, 1] == X2_test)
+
+        self.assertTrue(xtest and ytest)
+
+    def test_ndgrid_3D(self):
+        XYZ = ndgrid([self.a, self.b, self.c])
+
+        X1_test = np.array([1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3])
+        X2_test = np.array([1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2])
+        X3_test = np.array([1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4])
+
+        xtest = np.all(XYZ[:, 0] == X1_test)
+        ytest = np.all(XYZ[:, 1] == X2_test)
+        ztest = np.all(XYZ[:, 2] == X3_test)
+
+        self.assertTrue(xtest and ytest and ztest)
+
+if __name__ == '__main__':
+    unittest.main()
+

code/utils.py

@@ -1,4 +1,5 @@
 from numpy import *
+import numpy as np
 
 
 def diff(A, d):
@@ -43,35 +44,54 @@ def ave(A, d):
         print('d must be 1,2 or 3')
 
 
-def reshapeF(sp, d):
-    return reshape(sp, d, 'F')
+def reshapeF(x, size):
+    return np.reshape(x, size, order='F')
 
 
-def mkvc(A):
-    return reshape(A, [size(A), 1], 'F').flatten()
+def mkvc(x, numDims=1):
+    """Creates a vector with the number of dimension specified
+
+    e.g.:
+
+        a = np.array(1,2,3)
+
+        mkvc(a, 1).shape
+            > (3, )
+
+        mkvc(a, 2).shape
+            > (3, 1)
+
+        mkvc(a, 3).shape
+            > (3, 1, 1)
+
+    """
+    assert type(x) == np.ndarray, "Vector must be a numpy array"
+
+    if numDims == 1:
+        return x.flatten(order='F')
+    elif numDims == 2:
+        return x.flatten(order='F')[:, np.newaxis]
+    elif numDims == 3:
+        return x.flatten(order='F')[:, np.newaxis, np.newaxis]
 
 
-def ndgrid(x, y, z):
+def ndgrid(*args):
+    """Form tensorial grid for 1, 2 and 3 dimensions. Return X1,X2,X3 arrays depending on the dimension"""
 
-    n1 = size(x)
-    n2 = size(y)
-    n3 = size(z)
-    X = zeros([n1, n2, n3])
-    Y = zeros([n1, n2, n3])
-    Z = zeros([n1, n2, n3])
-    for i in range(0, n2):
-        for j in range(0, n3):
-            X[:, i, j] = x
+    # you can either pass a list [x1, x2, x3] or each seperately
+    if type(args[0]) == list:
+        xin = args[0]
+    else:
+        xin = args
 
-    for i in range(0, n1):
-        for j in range(0, n3):
-            Y[i, :, j] = y
-
-    for i in range(0, n1):
-        for j in range(0, n2):
-            Z[i, j, :] = z
-
-    return (X, Y, Z)
+    if len(xin) == 1:
+        return xin
+    elif len(xin) == 2:
+        X2, X1 = [mkvc(x) for x in np.broadcast_arrays(mkvc(xin[1], 1), mkvc(xin[0], 2))]
+        return np.c_[X1, X2]
+    elif len(xin) == 3:
+        X3, X2, X1 = [mkvc(x) for x in np.broadcast_arrays(mkvc(xin[2], 1), mkvc(xin[1], 2), mkvc(xin[0], 3))]
+        return np.c_[X1, X2, X3]
 
 
 def ind2sub(shape, ind):