Initial merge and minor refactor of simpegPF.

.gitignore

@@ -40,3 +40,4 @@ nosetests.xml
 docs/_build/
 Makefile
 docs/warnings.txt
+*.ipynb_checkpoints

.travis.yml

@@ -18,6 +18,7 @@ env:
     - TEST_DIR="tests/mesh tests/base tests/utils"
     - TEST_DIR=tests/em/fdem/inverse/derivs
     - TEST_DIR=tests/em/tdem
+    - TEST_DIR=tests/pf
     - TEST_DIR=tests/dcip
     - TEST_DIR=tests/flow
     - TEST_DIR=tests/mt

SimPEG/Examples/Mesh_Basic_Types.py

@@ -1,4 +1,5 @@
-from SimPEG import *
+from SimPEG import Mesh, Utils, np
+
 
 def run(plotIt=True):
     """
@@ -8,15 +9,15 @@ def run(plotIt=True):
         Here we show SimPEG used to create three different types of meshes.
 
     """
-    sz = [16,16]
+    sz = [16, 16]
     tM = Mesh.TensorMesh(sz)
     qM = Mesh.TreeMesh(sz)
     qM.refine(lambda cell: 4 if np.sqrt(((np.r_[cell.center]-0.5)**2).sum()) < 0.4 else 3)
-    rM = Mesh.CurvilinearMesh(Utils.meshutils.exampleLrmGrid(sz,'rotate'))
+    rM = Mesh.CurvilinearMesh(Utils.meshutils.exampleLrmGrid(sz, 'rotate'))
 
     if plotIt:
         import matplotlib.pyplot as plt
-        fig, axes = plt.subplots(1,3,figsize=(14,5))
+        fig, axes = plt.subplots(1, 3, figsize=(14, 5))
         opts = {}
         tM.plotGrid(ax=axes[0], **opts)
         axes[0].set_title('TensorMesh')

SimPEG/Examples/PF_Magnetics_Analytics.py

@@ -0,0 +1,65 @@
+from SimPEG import Mesh, np, PF
+
+
+def run(plotIt=True):
+    """
+        PF: Magnetics: Analytics
+        ========================
+
+        Comparing the magnetics field in Vancouver to Seoul
+
+    """
+
+    xr = np.linspace(-300, 300, 41)
+    yr = np.linspace(-300, 300, 41)
+    X, Y = np.meshgrid(xr, yr)
+    Z = np.ones((np.size(xr), np.size(yr)))*150
+
+    # Bz component in Korea
+    inckr = -8. + 3./60
+    deckr = 54. + 9./60
+    btotkr = 50898.6
+    Bokr = PF.MagAnalytics.IDTtoxyz(inckr, deckr, btotkr)
+
+    bx, by, bz = PF.MagAnalytics.MagSphereAnaFunA(
+        X, Y, Z, 100., 0., 0., 0., 0.01, Bokr, 'secondary'
+    )
+    Bzkr = np.reshape(bz, (np.size(xr), np.size(yr)), order='F')
+
+    # Bz component in Canada
+    incca = 16. + 49./60
+    decca = 70. + 19./60
+    btotca = 54692.1
+    Boca = PF.MagAnalytics.IDTtoxyz(incca, decca, btotca)
+
+    bx, by, bz = PF.MagAnalytics.MagSphereAnaFunA(
+        X, Y, Z, 100., 0., 0., 0., 0.01, Boca, 'secondary'
+    )
+    Bzca = np.reshape(bz, (np.size(xr), np.size(yr)), order='F')
+
+    if plotIt:
+        import matplotlib.pyplot as plt
+        from mpl_toolkits.axes_grid1 import make_axes_locatable
+        fig = plt.figure(figsize=(14, 5))
+
+        ax1 = plt.subplot(121)
+        dat1 = plt.imshow(Bzkr, extent=[min(xr), max(xr), min(yr), max(yr)])
+        divider = make_axes_locatable(ax1)
+        cax1 = divider.append_axes("right", size="5%", pad=0.05)
+        ax1.set_xlabel('East-West (m)')
+        ax1.set_ylabel('South-North (m)')
+        plt.colorbar(dat1, cax=cax1)
+        ax1.set_title('$B_z$ field at Seoul, South Korea')
+
+        ax2 = plt.subplot(122)
+        dat2 = plt.imshow(Bzca, extent=[min(xr), max(xr), min(yr), max(yr)])
+        divider = make_axes_locatable(ax2)
+        cax2 = divider.append_axes("right", size="5%", pad=0.05)
+        ax2.set_xlabel('East-West (m)')
+        ax2.set_ylabel('South-North (m)')
+        plt.colorbar(dat2, cax=cax2)
+        ax2.set_title('$B_z$ field at Vancouver, Canada')
+        plt.show()
+
+if __name__ == '__main__':
+    run()

SimPEG/Examples/__init__.py

@@ -20,9 +20,10 @@ import Mesh_QuadTree_HangingNodes
 import Mesh_Tensor_Creation
 import MT_1D_ForwardAndInversion
 import MT_3D_Foward
+import PF_Magnetics_Analytics
 import Utils_surface2ind_topo
 
-__examples__ = ["DC_Analytic_Dipole", "DC_Forward_PseudoSection", "EM_FDEM_1D_Inversion", "EM_FDEM_Analytic_MagDipoleWholespace", "EM_Schenkel_Morrison_Casing", "EM_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Inversion_IRLS", "Inversion_Linear", "Mesh_Basic_ForwardDC", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation", "MT_1D_ForwardAndInversion", "MT_3D_Foward", "Utils_surface2ind_topo"]
+__examples__ = ["DC_Analytic_Dipole", "DC_Forward_PseudoSection", "EM_FDEM_1D_Inversion", "EM_FDEM_Analytic_MagDipoleWholespace", "EM_Schenkel_Morrison_Casing", "EM_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Inversion_IRLS", "Inversion_Linear", "Mesh_Basic_ForwardDC", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation", "MT_1D_ForwardAndInversion", "MT_3D_Foward", "PF_Magnetics_Analytics", "Utils_surface2ind_topo"]
 
 ##### AUTOIMPORTS #####
 

SimPEG/PF/BaseGrav.py

@@ -0,0 +1,53 @@
+from SimPEG import Maps, Survey, Utils, np, sp
+from scipy.constants import mu_0
+import re
+
+
+class LinearSurvey(Survey.BaseSurvey):
+    """Base Magnetics Survey"""
+
+    rxLoc = None #: receiver locations
+    rxType = None #: receiver type
+
+    def __init__(self, srcField, **kwargs):
+        self.srcField = srcField
+        Survey.BaseSurvey.__init__(self, **kwargs)
+
+    def eval(self, u):
+        return u
+
+    @property
+    def nD(self):
+        return self.prob.G.shape[0]
+
+    @property
+    def nRx(self):
+        return self.srcField.rxList[0].locs.shape[0]
+    # def setBackgroundField(self, SrcField):
+
+    #     if getattr(self, 'B0', None) is None:
+    #         self._B0 = SrcField.param[0] * dipazm_2_xyz(SrcField.param[1],SrcField.param[2])
+
+    #     return self._B0
+
+
+class SrcField(Survey.BaseSrc):
+    """ Define the inducing field """
+
+    param = None #: Inducing field param (Amp, Incl, Decl)
+
+    def __init__(self, rxList, **kwargs):
+        super(SrcField, self).__init__(rxList, **kwargs)
+
+
+class RxObs(Survey.BaseRx):
+    """A station location must have be located in 3-D"""
+    def __init__(self, locsXYZ, **kwargs):
+        locs = locsXYZ
+        assert locsXYZ.shape[1] == 3, 'locs must in 3-D (x,y,z).'
+        super(RxObs, self).__init__(locs, 'tmi', storeProjections=False, **kwargs)
+
+    @property
+    def nD(self):
+        """Number of data in the receiver."""
+        return self.locs[0].shape[0]

SimPEG/PF/BaseMag.py

@@ -0,0 +1,194 @@
+from SimPEG import Maps, Survey, Utils, np, sp
+from scipy.constants import mu_0
+import re
+
+
+class BaseMagSurvey(Survey.BaseSurvey):
+    """Base Magnetics Survey"""
+
+    rxLoc = None   #: receiver locations
+    rxType = None   #: receiver type
+
+    def __init__(self, **kwargs):
+        Survey.BaseSurvey.__init__(self, **kwargs)
+
+    def setBackgroundField(self, Inc, Dec, Btot):
+
+        Bx = Btot*np.cos(Inc/180.*np.pi)*np.sin(Dec/180.*np.pi)
+        By = Btot*np.cos(Inc/180.*np.pi)*np.cos(Dec/180.*np.pi)
+        Bz = -Btot*np.sin(Inc/180.*np.pi)
+
+        self.B0 = np.r_[Bx, By, Bz]
+
+    @property
+    def Qfx(self):
+        if getattr(self, '_Qfx', None) is None:
+            self._Qfx = self.prob.mesh.getInterpolationMat(self.rxLoc, 'Fx')
+        return self._Qfx
+
+    @property
+    def Qfy(self):
+        if getattr(self, '_Qfy', None) is None:
+            self._Qfy = self.prob.mesh.getInterpolationMat(self.rxLoc, 'Fy')
+        return self._Qfy
+
+    @property
+    def Qfz(self):
+        if getattr(self, '_Qfz', None) is None:
+            self._Qfz = self.prob.mesh.getInterpolationMat(self.rxLoc, 'Fz')
+        return self._Qfz
+
+    def projectFields(self, u):
+        """
+            This function projects the fields onto the data space.
+
+            Especially, here for we use total magnetic intensity (TMI) data,
+            which is common in practice.
+
+            First we project our B on to data location
+
+            .. math::
+
+                \mathbf{B}_{rec} = \mathbf{P} \mathbf{B}
+
+            then we take the dot product between B and b_0
+
+            .. math ::
+
+                \\text{TMI} = \\vec{B}_s \cdot \hat{B}_0
+
+        """
+        # TODO: There can be some different tyes of data like |B| or B
+
+        bfx = self.Qfx*u['B']
+        bfy = self.Qfy*u['B']
+        bfz = self.Qfz*u['B']
+
+        # Generate unit vector
+        B0 = self.prob.survey.B0
+        Bot = np.sqrt(B0[0]**2+B0[1]**2+B0[2]**2)
+        box = B0[0]/Bot
+        boy = B0[1]/Bot
+        boz = B0[2]/Bot
+
+        # return bfx*box + bfx*boy + bfx*boz
+        return bfx*box + bfy*boy + bfz*boz
+
+    @Utils.count
+    def projectFieldsDeriv(self, B):
+        """
+            This function projects the fields onto the data space.
+
+            .. math::
+
+                \\frac{\partial d_\\text{pred}}{\partial \mathbf{B}} = \mathbf{P}
+
+            Especially, this function is for TMI data type
+
+        """
+        # Generate unit vector
+        B0 = self.prob.survey.B0
+        Bot = np.sqrt(B0[0]**2+B0[1]**2+B0[2]**2)
+        box = B0[0]/Bot
+        boy = B0[1]/Bot
+        boz = B0[2]/Bot
+
+        return self.Qfx*box+self.Qfy*boy+self.Qfz*boz
+
+    def projectFieldsAsVector(self, B):
+
+        bfx = self.Qfx*B
+        bfy = self.Qfy*B
+        bfz = self.Qfz*B
+
+        return np.r_[bfx, bfy, bfz]
+
+
+class LinearSurvey(Survey.BaseSurvey):
+    """Base Magnetics Survey"""
+
+    rxLoc = None #: receiver locations
+    rxType = None #: receiver type
+
+    def __init__(self, srcField, **kwargs):
+        self.srcField = srcField
+        Survey.BaseSurvey.__init__(self, **kwargs)
+
+    def eval(self, u):
+        return u
+
+    @property
+    def nD(self):
+        return self.prob.G.shape[0]
+
+    @property
+    def nRx(self):
+        return self.srcField.rxList[0].locs.shape[0]
+    # def setBackgroundField(self, SrcField):
+
+    #     if getattr(self, 'B0', None) is None:
+    #         self._B0 = SrcField.param[0] * dipazm_2_xyz(SrcField.param[1],SrcField.param[2])
+
+    #     return self._B0
+
+
+class SrcField(Survey.BaseSrc):
+    """ Define the inducing field """
+
+    param = None #: Inducing field param (Amp, Incl, Decl)
+
+    def __init__(self, rxList, **kwargs):
+        super(SrcField, self).__init__(rxList, **kwargs)
+
+
+class RxObs(Survey.BaseRx):
+    """A station location must have be located in 3-D"""
+    def __init__(self, locsXYZ, **kwargs):
+        locs = locsXYZ
+        assert locsXYZ.shape[1] == 3, 'locs must in 3-D (x,y,z).'
+        super(RxObs, self).__init__(locs, 'tmi', storeProjections=False, **kwargs)
+
+    @property
+    def nD(self):
+        """Number of data in the receiver."""
+        return self.locs[0].shape[0]
+
+
+class MagSurveyBx(object):
+    """docstring for MagSurveyBx"""
+    def __init__(self, **kwargs):
+        Survey.BaseData.__init__(self, **kwargs)
+
+    def projectFields(self, B):
+        bfx = self.Qfx*B
+        return bfx
+
+
+class BaseMagMap(Maps.IdentityMap):
+    """BaseMagMap"""
+
+    def __init__(self, mesh, **kwargs):
+        Maps.IdentityMap.__init__(self, mesh)
+
+    def _transform(self, m):
+
+        return mu_0*(1 + m)
+
+    def deriv(self, m):
+
+        return mu_0*sp.identity(self.nP)
+
+
+class WeightMap(Maps.IdentityMap):
+    """Weighted Map for distributed parameters"""
+
+    def __init__(self, nP, weight, **kwargs):
+        Maps.IdentityMap.__init__(self, nP)
+        self.mesh = None
+        self.weight = weight
+
+    def _transform(self, m):
+        return m*self.weight
+
+    def deriv(self, m):
+        return Utils.sdiag(self.weight)

SimPEG/PF/Gravity.py

@@ -0,0 +1,491 @@
+from SimPEG import *
+import BaseGrav as GRAV
+import re
+
+
+class GravityIntegral(Problem.BaseProblem):
+
+    # surveyPair = Survey.LinearSurvey
+
+    storeG = True #: Store the forward matrix by default, otherwise just compute d
+    actInd = None #: Active cell indices provided
+
+    def __init__(self, mesh, mapping=None, **kwargs):
+        Problem.BaseProblem.__init__(self, mesh, mapping=mapping, **kwargs)
+
+    def fwr_op(self):
+        # Add forward function
+        # kappa = self.curModel.kappa TODO
+        sus = self.mapping*self.curModel
+        return self.G.dot(sus)
+
+    def fields(self, m):
+        self.curModel = m
+        total = np.zeros(self.survey.nRx)
+        induced = self.fwr_op()
+        # rem = self.rem
+
+        if induced is not None:
+            total += induced
+
+        return total
+
+        # return self.G.dot(self.mapping*(m))
+
+    def Jvec(self, m, v, f=None):
+        dmudm = self.mapping.deriv(m)
+        return self.G.dot(dmudm*v)
+
+    def Jtvec(self, m, v, f=None):
+        dmudm = self.mapping.deriv(m)
+        return dmudm.T * (self.G.T.dot(v))
+
+    @property
+    def G(self):
+        if not self.ispaired:
+            raise Exception('Need to pair!')
+
+        if getattr(self, '_G', None) is None:
+            self._G = self.Intrgl_Fwr_Op( 'z' )
+
+        return self._G
+
+    def Intrgl_Fwr_Op(self, flag):
+
+        """
+
+        Gravity forward operator in integral form
+
+        flag        = 'z' | 'xyz'
+
+        Return
+        _G        = Linear forward modeling operation
+
+        Created on March, 15th 2016
+
+        @author: dominiquef
+
+         """
+        # Find non-zero cells
+        # inds = np.nonzero(actv)[0]
+        if getattr(self, 'actInd', None) is not None:
+
+            if self.actInd.dtype=='bool':
+                inds = np.asarray([inds for inds, elem in enumerate(self.actInd, 1) if elem], dtype = int) - 1
+            else:
+                inds = self.actInd
+
+        else:
+
+            inds = np.asarray(range(self.mesh.nC))
+
+        nC = len(inds)
+
+        # Create active cell projector
+        P = sp.csr_matrix(
+            (np.ones(nC), (inds, range(nC))),
+            shape=(self.mesh.nC, nC)
+        )
+
+        # Create vectors of nodal location (lower and upper corners for each cell)
+        xn = self.mesh.vectorNx
+        yn = self.mesh.vectorNy
+        zn = self.mesh.vectorNz
+
+        yn2, xn2, zn2 = np.meshgrid(yn[1:], xn[1:], zn[1:])
+        yn1, xn1, zn1 = np.meshgrid(yn[0:-1], xn[0:-1], zn[0:-1])
+
+        Yn = P.T*np.c_[mkvc(yn1), mkvc(yn2)]
+        Xn = P.T*np.c_[mkvc(xn1), mkvc(xn2)]
+        Zn = P.T*np.c_[mkvc(zn1), mkvc(zn2)]
+
+        rxLoc = self.survey.srcField.rxList[0].locs
+        ndata = rxLoc.shape[0]
+
+        # Pre-allocate space and create magnetization matrix if required
+        # Pre-allocate space
+        if flag == 'z':
+
+            G = np.zeros((ndata, nC))
+
+        elif flag == 'xyz':
+
+            G = np.zeros((int(3*ndata), nC))
+
+        else:
+
+            print """Flag must be either 'z' | 'xyz', please revised"""
+            return
+
+
+        # Loop through all observations and create forward operator (ndata-by-nC)
+        print "Begin calculation of forward operator: " + flag
+
+        # Add counter to dsiplay progress. Good for large problems
+        count = -1;
+        for ii in range(ndata):
+
+            if flag=='z':
+                tt = get_T_mat(Xn, Yn, Zn, rxLoc[ii, :])
+                G[ii, :] = tt
+
+            elif flag == 'xyz':
+                print "Sorry 3-component not implemented yet"
+
+            # Display progress
+            count = progress(ii, count, ndata)
+
+        print "Done 100% ...forward operator completed!!\n"
+
+        return G
+
+
+def get_T_mat(Xn, Yn, Zn, rxLoc):
+    """
+    Load in the active nodes of a tensor mesh and computes the gravity tensor
+    for a given observation location rxLoc[obsx, obsy, obsz]
+
+    INPUT:
+    Xn, Yn, Zn: Node location matrix for the lower and upper most corners of
+                all cells in the mesh shape[nC,2]
+    M
+    OUTPUT:
+    Tx = [Txx Txy Txz]
+    Ty = [Tyx Tyy Tyz]
+    Tz = [Tzx Tzy Tzz]
+
+    where each elements have dimension 1-by-nC.
+    Only the upper half 5 elements have to be computed since symetric.
+    Currently done as for-loops but will eventually be changed to vector
+    indexing, once the topography has been figured out.
+
+    """
+    NewtG=6.6738e-3
+    eps = 1e-10 # add a small value to the locations to avoid /0
+
+    nC = Xn.shape[0]
+
+    # Pre-allocate space for 1D array
+    T = np.zeros((1,nC))
+
+    dz = rxLoc[2] - Zn + eps
+
+    dy = Yn - rxLoc[1] + eps
+
+    dx = Xn - rxLoc[0] + eps
+
+    # Compute contribution from each corners
+    for aa in range(2):
+        for bb in range(2):
+            for cc in range(2):
+
+                r = (
+                        dx[:, aa] ** 2 +
+                        dy[:, bb] ** 2 +
+                        dz[:, cc] ** 2
+                    ) ** (0.50)
+
+                T = T - NewtG * (-1) ** aa * (-1) ** bb * (-1) ** cc * (
+                    dx[:, aa] * np.log(dy[:, bb] + r) +
+                    dy[:, bb] * np.log(dx[:, aa] + r) -
+                    dz[:, cc] * np.arctan(
+                        dx[:, aa] * dy[:, bb] / (dz[:, cc] * r)
+                    )
+                )
+
+    return T
+
+
+def progress(iter, prog, final):
+    """
+    progress(iter,prog,final)
+
+    Function measuring the progress of a process and print to screen the %.
+    Useful to estimate the remaining runtime of a large problem.
+
+    Created on Dec, 20th 2015
+
+    @author: dominiquef
+    """
+    arg = np.floor(float(iter)/float(final)*10.)
+
+    if  arg > prog:
+
+        strg = "Done " + str(arg*10) + " %"
+        print strg
+        prog = arg
+
+    return prog
+
+
+def writeUBCobs(filename, survey, d):
+    """
+    writeUBCobs(filename,survey,d)
+
+    Function writing an observation file in UBC-GRAV3D format.
+
+    INPUT
+    filename    : Name of out file including directory
+    survey
+    flag          : dobs | dpred
+
+    OUTPUT
+    Obsfile
+
+    """
+
+    rxLoc = survey.srcField.rxList[0].locs
+
+    wd = survey.std
+
+    data = np.c_[rxLoc , d , wd]
+
+    with file(filename,'w') as fid:
+        fid.write('%i\n' %len(d) )
+        np.savetxt(fid, data, fmt='%e', delimiter=' ', newline='\n')
+
+
+    print "Observation file saved to: " + filename
+
+
+def getActiveTopo(mesh, topo, flag):
+    """
+    getActiveTopo(mesh,topo)
+
+    Function creates an active cell model from topography
+
+    INPUT
+    mesh        : Mesh in SimPEG format
+    topo        : Scatter points defining topography [x,y,z]
+
+    OUTPUT
+    actv        : Active cell model
+
+    """
+    import scipy.interpolate as interpolation
+
+    if flag == 'N':
+        Zn = np.zeros((mesh.nNx, mesh.nNy))
+        # wght    = np.zeros((mesh.nNx,mesh.nNy))
+        cx = mesh.vectorNx
+        cy = mesh.vectorNy
+
+    F = interpolation.NearestNDInterpolator(topo[:, 0:2], topo[:, 2])
+    [Y, X] = np.meshgrid(cy, cx)
+
+    Zn = F(X, Y)
+
+    actv = np.zeros((mesh.nCx, mesh.nCy, mesh.nCz))
+
+    if flag == 'N':
+        Nz = mesh.vectorNz[1:]
+
+    for jj in range(mesh.nCy):
+
+        for ii in range(mesh.nCx):
+
+            temp = [kk for kk in range(len(Nz)) if np.all(Zn[ii:(ii+2), jj:(jj+2)] > Nz[kk]) ]
+            actv[ii, jj, temp] = 1
+
+    actv = mkvc(actv == 1)
+
+    inds = np.asarray([inds for inds, elem in enumerate(actv, 1) if elem], dtype = int) - 1
+
+    return inds
+
+def plot_obs_2D(survey,varstr):
+    """ Function plot_obs(rxLoc,d,wd)
+    Generate a 2d interpolated plot from scatter points of data
+
+    INPUT
+    rxLoc       : Observation locations [x,y,z]
+    d           : Data vector
+    wd          : Uncertainty vector
+
+    OUTPUT
+    figure()
+
+    Created on Dec, 27th 2015
+
+    @author: dominiquef
+
+    """
+
+    from scipy.interpolate import griddata
+    import pylab as plt
+
+    rxLoc   = survey.srcField.rxList[0].locs
+    d       = survey.dobs
+    wd      = survey.std
+
+    # Create grid of points
+    x = np.linspace(rxLoc[:,0].min(), rxLoc[:,0].max(), 100)
+    y = np.linspace(rxLoc[:,1].min(), rxLoc[:,1].max(), 100)
+
+    X, Y = np.meshgrid(x,y)
+
+    # Interpolate
+    d_grid = griddata(rxLoc[:,0:2],d,(X,Y), method ='linear')
+
+    # Plot result
+    plt.figure()
+    plt.subplot()
+    plt.imshow(d_grid, extent=[x.min(), x.max(), y.min(), y.max()],origin = 'lower')
+    plt.colorbar(fraction=0.02)
+    plt.contour(X,Y, d_grid,10)
+    plt.scatter(rxLoc[:,0],rxLoc[:,1], c=d, s=20)
+    plt.title(varstr)
+    plt.gca().set_aspect('equal', adjustable='box')
+
+def readUBCgravObs(obs_file):
+
+    """
+    Read UBC grav file format
+
+    INPUT:
+    :param fileName, path to the UBC obs grav file
+
+    OUTPUT:
+    :param survey
+
+    """
+
+    fid = open(obs_file,'r')
+
+    # First line has the number of rows
+    line = fid.readline()
+    ndat = np.array(line.split(),dtype=int)
+
+    # Pre-allocate space for obsx, obsy, obsz, data, uncert
+    line = fid.readline()
+    temp = np.array(line.split(),dtype=float)
+
+    d  = np.zeros(ndat, dtype=float)
+    wd = np.zeros(ndat, dtype=float)
+    locXYZ = np.zeros( (ndat,3), dtype=float)
+
+    for ii in range(ndat):
+
+        temp = np.array(line.split(),dtype=float)
+        locXYZ[ii,:] = temp[:3]
+        d[ii] = temp[3]
+        wd[ii] = temp[4]
+        line = fid.readline()
+
+    rxLoc = GRAV.RxObs(locXYZ)
+    srcField = GRAV.SrcField([rxLoc])
+    survey = GRAV.LinearSurvey(srcField)
+    survey.dobs =  d
+    survey.std =  wd
+    return survey
+
+
+def read_GRAVinv_inp(input_file):
+    """Read input files for forward modeling MAG data with integral form
+    INPUT:
+    input_file: File name containing the forward parameter
+
+    OUTPUT:
+    mshfile
+    obsfile
+    topofile
+    start model
+    ref model
+    weightfile
+    chi_target
+    as, ax ,ay, az
+    upper, lower bounds
+    lp, lqx, lqy, lqz
+
+    # All files should be in the working directory, otherwise the path must
+    # be specified.
+
+    Created on Dec 21th, 2015
+
+    @author: dominiquef
+    """
+
+
+    fid = open(input_file,'r')
+
+    # Line 1
+    line = fid.readline()
+    l_input  = line.split('!')
+    mshfile = l_input[0].rstrip()
+
+    # Line 2
+    line = fid.readline()
+    l_input  = line.split('!')
+    obsfile = l_input[0].rstrip()
+
+    # Line 3
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    if l_input=='null':
+        topofile = []
+
+    else:
+        topofile = l_input[0].rstrip()
+
+
+    # Line 4
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    if l_input[0]=='VALUE':
+        mstart = float(l_input[1])
+
+    else:
+        mstart = l_input[0].rstrip()
+
+    # Line 5
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    if l_input[0]=='VALUE':
+        mref = float(l_input[1])
+
+    else:
+        mref = l_input[0].rstrip()
+
+
+    # Line 7
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    if l_input[0]=='DEFAULT':
+        wgtfile = None
+
+    else:
+        wgtfile = l_input[0].rstrip()
+
+    # Line 8
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    chi = float(l_input[0])
+
+    # Line 9
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    val = np.array(l_input[0:4])
+    alphas = val.astype(np.float)
+
+    # Line 10
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    if l_input[0]=='VALUE':
+        val   = np.array(l_input[1:3])
+        bounds = val.astype(np.float)
+
+    else:
+        bounds = l_input[0].rstrip()
+
+    # Line 11
+    line = fid.readline()
+    l_input = re.split('[!\s]',line)
+    if l_input[0]=='VALUE':
+        val   = np.array(l_input[1:6])
+        lpnorms = val.astype(np.float)
+
+    else:
+        lpnorms = l_input[0].rstrip()
+
+    return mshfile, obsfile, topofile, mstart, mref, wgtfile, chi, alphas, bounds, lpnorms
+

SimPEG/PF/GravityDriver.py

@@ -0,0 +1,295 @@
+import re, os
+from SimPEG import Mesh, np, Utils
+import BaseGrav, Gravity
+
+
+class GravityDriver_Inv(object):
+    """docstring for GravityDriver_Inv"""
+
+    def __init__(self, input_file=None):
+        if input_file is not None:
+            self.basePath = os.path.sep.join(input_file.split(os.path.sep)[:-1])
+            if len(self.basePath) > 0:
+                self.basePath += os.path.sep
+            self.readDriverFile(input_file.split(os.path.sep)[-1])
+
+    def readDriverFile(self, input_file):
+        """
+            Read input files for forward modeling GRAV data with integral form
+            INPUT:
+            input_file: File name containing the forward parameter
+
+            OUTPUT:
+            mshfile
+            obsfile
+            topofile
+            start model
+            ref model
+            active cells model
+            weightfile
+            chi_target
+            as, ax ,ay, az
+            upper, lower bounds
+            lp, lqx, lqy, lqz
+            eps_p, eps_q
+            # All files should be in the working directory, otherwise the path must
+            # be specified.
+
+        """
+
+        fid = open(self.basePath + input_file, 'r')
+
+        # Line 1
+        line = fid.readline()
+        l_input  = line.split('!')
+        mshfile = l_input[0].rstrip()
+
+        # Line 2
+        line = fid.readline()
+        l_input  = line.split('!')
+        obsfile = l_input[0].rstrip()
+
+        # Line 3
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        if l_input=='null':
+            topofile = []
+
+        else:
+            topofile = l_input[0].rstrip()
+
+
+        # Line 4
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        if l_input[0]=='VALUE':
+            mstart = float(l_input[1])
+
+        else:
+            mstart = l_input[0].rstrip()
+
+        # Line 5
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input[0]=='VALUE':
+            mref = float(l_input[1])
+
+        else:
+            mref = l_input[0].rstrip()
+
+        # Line 6
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        if l_input[0]=='VALUE':
+            staticInput = float(l_input[1])
+
+        elif l_input[0]=='DEFAULT':
+            staticInput = None
+
+        else:
+            staticInput = l_input[0].rstrip()
+
+        # Line 7
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        if l_input=='DEFAULT':
+            wgtfile = []
+
+        else:
+            wgtfile = l_input[0].rstrip()
+
+        # Line 8
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        chi = float(l_input[0])
+
+        # Line 9
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        val = np.array(l_input[0:4])
+        alphas = val.astype(np.float)
+
+        # Line 10
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        if l_input[0]=='VALUE':
+            val   = np.array(l_input[1:3])
+            bounds = val.astype(np.float)
+
+        else:
+            bounds = l_input[0].rstrip()
+
+        # Line 11
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        if l_input[0]=='VALUE':
+            val   = np.array(l_input[1:6])
+            lpnorms = val.astype(np.float)
+
+        else:
+            lpnorms = l_input[0].rstrip()
+
+        # Line 12
+        line = fid.readline()
+        l_input = re.split('[!\s]', line)
+        if l_input[0]=='VALUE':
+            val   = np.array(l_input[1:3])
+            eps = val.astype(np.float)
+
+        else:
+            eps = [None, None]
+
+        self.mshfile  = mshfile
+        self.obsfile  = obsfile
+        self.topofile = topofile
+        self.mstart   = mstart
+        self._mrefInput = mref
+        self._staticInput = staticInput
+        self.wgtfile  = wgtfile
+        self.chi      = chi
+        self.alphas   = alphas
+        self.bounds   = bounds
+        self.lpnorms  = lpnorms
+        self.eps      = eps
+
+    @property
+    def mesh(self):
+        if getattr(self, '_mesh', None) is None:
+            self._mesh = Mesh.TensorMesh.readUBC(self.basePath + self.mshfile)
+        return self._mesh
+
+    @property
+    def survey(self):
+        if getattr(self, '_survey', None) is None:
+            self._survey = self.readGravityObservations(self.basePath + self.obsfile)
+        return self._survey
+
+    @property
+    def activeCells(self):
+        if getattr(self, '_activeCells', None) is None:
+            if self.topofile == 'null':
+                self._activeCells = np.arange(mesh.nC)
+            else:
+                topo = np.genfromtxt(self.basePath + self.topofile, skip_header=1)
+                # Find the active cells
+                active = Utils.surface2ind_topo(self.mesh,topo,'N')
+                inds = np.asarray([inds for inds, elem in enumerate(active, 1) if elem], dtype = int) - 1
+                self._activeCells = inds
+
+        return self._activeCells
+
+    @property
+    def staticCells(self):
+        if getattr(self, '_staticCells', None) is None:
+
+            if getattr(self, '_staticInput', None) is None:
+                # All cells are dynamic: 1's
+                self._dynamicCells = np.arange(len(self.m0))
+                self._staticCells = []
+
+            # Cells with specific value are static: 0's
+            else:
+                if isinstance(self._staticInput, float):
+                    staticCells = self.m0 == self._staticInput
+
+                else:
+                    # Read from file active cells with 0:air, 1:dynamic, -1 static
+                    staticCells = Mesh.TensorMesh.readModelUBC(self.mesh, self.basePath + self._staticInput)
+                    staticCells = staticCells[self.activeCells] == -1
+
+                inds = np.asarray([inds for inds, elem in enumerate(staticCells, 1) if elem], dtype = int) - 1
+                self._staticCells = inds
+
+        return self._staticCells
+
+    @property
+    def dynamicCells(self):
+        if getattr(self, '_dynamicCells', None) is None:
+
+            if getattr(self, '_staticInput', None) is None:
+                # All cells are dynamic: 1's
+                self._dynamicCells = np.arange(len(self.m0))
+
+            # Cells with specific value are static: 0's
+            else:
+                if isinstance(self._staticInput, float):
+                    dynamicCells = self.m0 != self._staticInput
+
+                else:
+                    # Read from file active cells with 0:air, 1:dynamic, -1 static
+                    dynamicCells = Mesh.TensorMesh.readModelUBC(self.mesh, self.basePath + self._staticInput)
+                    dynamicCells = dynamicCells[self.activeCells] == 1
+
+                inds = np.asarray([inds for inds, elem in enumerate(dynamicCells, 1) if elem], dtype = int) - 1
+                self._dynamicCells = inds
+
+        return self._dynamicCells
+
+    @property
+    def nC(self):
+        if getattr(self, '_nC', None) is None:
+            self._nC = len(self.activeCells)
+        return self._nC
+
+    @property
+    def m0(self):
+        if getattr(self, '_m0', None) is None:
+            if isinstance(self.mstart, float):
+                self._m0 = np.ones(self.nC) * self.mstart
+            else:
+
+                self._m0 = Mesh.TensorMesh.readModelUBC(self.mesh, self.basePath + self.mstart)
+                self._m0 = self._m0[self.activeCells]
+
+        return self._m0
+
+    @property
+    def mref(self):
+        if getattr(self, '_mref', None) is None:
+            if isinstance(self._mrefInput, float):
+                self._mref = np.ones(self.nC) * self._mrefInput
+            else:
+                self._mref = Mesh.TensorMesh.readModelUBC(self.mesh, self.basePath + self._mrefInput)
+                self._mref = self._mref[self.activeCells]
+        return self._mref
+
+    def readGravityObservations(self, obs_file):
+        """
+        Read UBC grav file format
+
+        INPUT:
+        :param fileName, path to the UBC obs grav file
+
+        OUTPUT:
+        :param survey
+
+        """
+
+        fid = open(obs_file,'r')
+
+        # First line has the number of rows
+        line = fid.readline()
+        ndat = np.array(line.split(),dtype=int)
+
+        # Pre-allocate space for obsx, obsy, obsz, data, uncert
+        line = fid.readline()
+        temp = np.array(line.split(),dtype=float)
+
+        d  = np.zeros(ndat, dtype=float)
+        wd = np.zeros(ndat, dtype=float)
+        locXYZ = np.zeros( (ndat,3), dtype=float)
+
+        for ii in range(ndat):
+
+            temp = np.array(line.split(),dtype=float)
+            locXYZ[ii,:] = temp[:3]
+            d[ii] = temp[3]
+            wd[ii] = temp[4]
+            line = fid.readline()
+
+        rxLoc = BaseGrav.RxObs(locXYZ)
+        srcField = BaseGrav.SrcField([rxLoc])
+        survey = BaseGrav.LinearSurvey(srcField)
+        survey.dobs =  d
+        survey.std =  wd
+        return survey

SimPEG/PF/MagAnalytics.py

@@ -0,0 +1,278 @@
+from scipy.constants import mu_0
+from SimPEG import *
+from SimPEG.Utils import kron3, speye, sdiag
+import matplotlib.pyplot as plt
+
+
+def spheremodel(mesh, x0, y0, z0, r):
+    """
+        Generate model indicies for sphere
+        - (x0, y0, z0 ): is the center location of sphere
+        - r: is the radius of the sphere
+        - it returns logical indicies of cell-center model
+    """
+    ind = np.sqrt( (mesh.gridCC[:,0]-x0)**2+(mesh.gridCC[:,1]-y0)**2+(mesh.gridCC[:,2]-z0)**2 ) < r
+    return ind
+
+
+def MagSphereAnaFun(x, y, z, R, x0, y0, z0, mu1, mu2, H0, flag='total'):
+    """
+        test
+        Analytic function for Magnetics problem. The set up here is
+        magnetic sphere in whole-space assuming that the inducing field is oriented in the x-direction.
+
+        * (x0,y0,z0)
+        * (x0, y0, z0 ): is the center location of sphere
+        * r: is the radius of the sphere
+
+    .. math::
+
+        \mathbf{H}_0 = H_0\hat{x}
+
+
+    """
+
+    if (~np.size(x)==np.size(y)==np.size(z)):
+        print "Specify same size of x, y, z"
+        return
+    dim = x.shape
+    x = Utils.mkvc(x)
+    y = Utils.mkvc(y)
+    z = Utils.mkvc(z)
+
+    ind = np.sqrt((x-x0)**2+(y-y0)**2+(z-z0)**2 ) < R
+    r = Utils.mkvc(np.sqrt((x-x0)**2+(y-y0)**2+(z-z0)**2 ))
+    Bx = np.zeros(x.size)
+    By = np.zeros(x.size)
+    Bz = np.zeros(x.size)
+
+    # Inside of the sphere
+    rf2 = 3*mu1/(mu2+2*mu1)
+    if flag is 'total' and any(ind):
+        Bx[ind] = mu2*H0*(rf2)
+    elif (flag == 'secondary'):
+        Bx[ind] = mu2*H0*(rf2)-mu1*H0
+
+    By[ind] = 0.
+    Bz[ind] = 0.
+    # Outside of the sphere
+    rf1 = (mu2-mu1)/(mu2+2*mu1)
+    if (flag == 'total'):
+        Bx[~ind] = mu1*(H0+H0/r[~ind]**5*(R**3)*rf1*(2*(x[~ind]-x0)**2-(y[~ind]-y0)**2-(z[~ind]-z0)**2))
+    elif (flag == 'secondary'):
+        Bx[~ind] = mu1*(H0/r[~ind]**5*(R**3)*rf1*(2*(x[~ind]-x0)**2-(y[~ind]-y0)**2-(z[~ind]-z0)**2))
+
+    By[~ind] = mu1*(H0/r[~ind]**5*(R**3)*rf1*(3*(x[~ind]-x0)*(y[~ind]-y0)))
+    Bz[~ind] = mu1*(H0/r[~ind]**5*(R**3)*rf1*(3*(x[~ind]-x0)*(z[~ind]-z0)))
+    return np.reshape(Bx, x.shape, order='F'), np.reshape(By, x.shape, order='F'), np.reshape(Bz, x.shape, order='F')
+
+
+def CongruousMagBC(mesh, Bo, chi):
+    """
+        Computing boundary condition using Congrous sphere method.
+        This is designed for secondary field formulation.
+
+        >> Input
+
+        * mesh:   Mesh class
+        * Bo:     np.array([Box, Boy, Boz]): Primary magnetic flux
+        * chi:    susceptibility at cell volume
+
+        .. math::
+
+            \\vec{B}(r) = \\frac{\mu_0}{4\pi} \\frac{m}{ \| \\vec{r} - \\vec{r}_0\|^3}[3\hat{m}\cdot\hat{r}-\hat{m}]
+
+    """
+
+    ind = chi > 0.
+    V = mesh.vol[ind].sum()
+
+    gamma = 1/V*(chi*mesh.vol).sum() # like a mass!
+
+    Bot = np.sqrt(sum(Bo**2))
+    mx = Bo[0]/Bot
+    my = Bo[1]/Bot
+    mz = Bo[2]/Bot
+
+    mom = 1/mu_0*Bot*gamma*V/(1+gamma/3)
+    xc = sum(chi[ind]*mesh.gridCC[:,0][ind])/sum(chi[ind])
+    yc = sum(chi[ind]*mesh.gridCC[:,1][ind])/sum(chi[ind])
+    zc = sum(chi[ind]*mesh.gridCC[:,2][ind])/sum(chi[ind])
+
+    indxd, indxu, indyd, indyu, indzd, indzu =  mesh.faceBoundaryInd
+
+    const = mu_0/(4*np.pi)*mom
+    rfun = lambda x: np.sqrt((x[:,0]-xc)**2 + (x[:,1]-yc)**2 + (x[:,2]-zc)**2)
+
+    mdotrx = (mx*(mesh.gridFx[(indxd|indxu),0]-xc)/rfun(mesh.gridFx[(indxd|indxu),:]) +
+              my*(mesh.gridFx[(indxd|indxu),1]-yc)/rfun(mesh.gridFx[(indxd|indxu),:]) +
+              mz*(mesh.gridFx[(indxd|indxu),2]-zc)/rfun(mesh.gridFx[(indxd|indxu),:]))
+
+    Bbcx = const/(rfun(mesh.gridFx[(indxd|indxu),:])**3)*(3*mdotrx*(mesh.gridFx[(indxd|indxu),0]-xc)/rfun(mesh.gridFx[(indxd|indxu),:])-mx)
+
+    mdotry = (mx*(mesh.gridFy[(indyd|indyu),0]-xc)/rfun(mesh.gridFy[(indyd|indyu),:]) +
+              my*(mesh.gridFy[(indyd|indyu),1]-yc)/rfun(mesh.gridFy[(indyd|indyu),:]) +
+              mz*(mesh.gridFy[(indyd|indyu),2]-zc)/rfun(mesh.gridFy[(indyd|indyu),:]))
+
+    Bbcy = const/(rfun(mesh.gridFy[(indyd|indyu),:])**3)*(3*mdotry*(mesh.gridFy[(indyd|indyu),1]-yc)/rfun(mesh.gridFy[(indyd|indyu),:])-my)
+
+    mdotrz = (mx*(mesh.gridFz[(indzd|indzu),0]-xc)/rfun(mesh.gridFz[(indzd|indzu),:])  +
+              my*(mesh.gridFz[(indzd|indzu),1]-yc)/rfun(mesh.gridFz[(indzd|indzu),:]) +
+              mz*(mesh.gridFz[(indzd|indzu),2]-zc)/rfun(mesh.gridFz[(indzd|indzu),:]))
+
+    Bbcz = const/(rfun(mesh.gridFz[(indzd|indzu),:])**3)*(3*mdotrz*(mesh.gridFz[(indzd|indzu),2]-zc)/rfun(mesh.gridFz[(indzd|indzu),:])-mz)
+
+    return np.r_[Bbcx, Bbcy, Bbcz], (1/gamma-1/(3+gamma))*1/V
+
+
+def MagSphereAnaFunA(x, y, z, R, xc, yc, zc, chi, Bo, flag):
+    """
+        Computing boundary condition using Congrous sphere method.
+        This is designed for secondary field formulation.
+        >> Input
+        mesh:   Mesh class
+        Bo:     np.array([Box, Boy, Boz]): Primary magnetic flux
+        Chi:    susceptibility at cell volume
+
+        .. math::
+
+            \\vec{B}(r) = \\frac{\mu_0}{4\pi}\\frac{m}{\| \\vec{r}-\\vec{r}_0\|^3}[3\hat{m}\cdot\hat{r}-\hat{m}]
+
+    """
+    if (~np.size(x)==np.size(y)==np.size(z)):
+        print "Specify same size of x, y, z"
+        return
+    dim = x.shape
+    x = Utils.mkvc(x)
+    y = Utils.mkvc(y)
+    z = Utils.mkvc(z)
+
+    Bot = np.sqrt(sum(Bo**2))
+    mx = Bo[0]/Bot
+    my = Bo[1]/Bot
+    mz = Bo[2]/Bot
+
+    ind = np.sqrt((x-xc)**2+(y-yc)**2+(z-zc)**2 ) < R
+
+    Bx = np.zeros(x.size)
+    By = np.zeros(x.size)
+    Bz = np.zeros(x.size)
+
+    # Inside of the sphere
+    rf2 = 3/(chi+3)*(1+chi)
+    if (flag == 'total'):
+        Bx[ind] = Bo[0]*(rf2)
+        By[ind] = Bo[1]*(rf2)
+        Bz[ind] = Bo[2]*(rf2)
+    elif (flag == 'secondary'):
+        Bx[ind] = Bo[0]*(rf2)-Bo[0]
+        By[ind] = Bo[1]*(rf2)-Bo[1]
+        Bz[ind] = Bo[2]*(rf2)-Bo[2]
+
+    r = Utils.mkvc(np.sqrt((x-xc)**2+(y-yc)**2+(z-zc)**2 ))
+    V = 4*np.pi*R**3/3
+    mom = Bot/mu_0*chi/(1+chi/3)*V
+    const = mu_0/(4*np.pi)*mom
+    mdotr = (mx*(x[~ind]-xc)/r[~ind] + my*(y[~ind]-yc)/r[~ind] + mz*(z[~ind]-zc)/r[~ind])
+    Bx[~ind] = const/(r[~ind]**3)*(3*mdotr*(x[~ind]-xc)/r[~ind]-mx)
+    By[~ind] = const/(r[~ind]**3)*(3*mdotr*(y[~ind]-yc)/r[~ind]-my)
+    Bz[~ind] = const/(r[~ind]**3)*(3*mdotr*(z[~ind]-zc)/r[~ind]-mz)
+
+
+    return Bx, By, Bz
+
+
+def IDTtoxyz(Inc, Dec, Btot):
+    """
+        Convert from Inclination, Declination, Total  intensity of earth field to x, y, z
+    """
+    Bx = Btot*np.cos(Inc/180.*np.pi)*np.sin(Dec/180.*np.pi)
+    By = Btot*np.cos(Inc/180.*np.pi)*np.cos(Dec/180.*np.pi)
+    Bz = -Btot*np.sin(Inc/180.*np.pi)
+
+    return np.r_[Bx, By, Bz]
+
+
+def MagSphereFreeSpace(x, y, z, R, xc, yc, zc, chi, Bo):
+    """
+        Computing boundary condition using Congrous sphere method.
+        This is designed for secondary field formulation.
+        >> Input
+        mesh:   Mesh class
+        Bo:     np.array([Box, Boy, Boz]): Primary magnetic flux
+        Chi:    susceptibility at cell volume
+
+        .. math::
+
+            \\vec{B}(r) = \\frac{\mu_0}{4\pi}\\frac{m}{\| \\vec{r}-\\vec{r}_0\|^3}[3\hat{m}\cdot\hat{r}-\hat{m}]
+
+    """
+    if (~np.size(x)==np.size(y)==np.size(z)):
+        print "Specify same size of x, y, z"
+        return
+
+    x = Utils.mkvc(x)
+    y = Utils.mkvc(y)
+    z = Utils.mkvc(z)
+
+    nobs = len(x)
+
+    Bot = np.sqrt(sum(Bo**2))
+
+    mx = np.ones([nobs]) * Bo[0,0] *  R**3 / 3. * chi
+    my = np.ones([nobs]) * Bo[0,1] *  R**3 / 3. * chi
+    mz = np.ones([nobs]) * Bo[0,2] *  R**3 / 3. * chi
+
+    M = np.c_[mx, my, mz]
+
+    rx = (x - xc)
+    ry = (y - yc)
+    rz = (zc - z)
+
+    rvec = np.c_[rx, ry, rz]
+    r = np.sqrt((rx)**2+(ry)**2+(rz)**2 )
+
+    B = -Utils.sdiag(1./r**3)*M + Utils.sdiag((3 * np.sum(M*rvec,axis=1))/r**5)*rvec
+
+    Bx = B[:,0]
+    By = B[:,1]
+    Bz = B[:,2]
+
+    return Bx, By, Bz
+
+if __name__ == '__main__':
+
+    hxind = [(0,25,1.3),(21, 12.5),(0,25,1.3)]
+    hyind = [(0,25,1.3),(21, 12.5),(0,25,1.3)]
+    hzind = [(0,25,1.3),(20, 12.5),(0,25,1.3)]
+    # hx, hy, hz = Utils.meshTensors(hxind, hyind, hzind)
+    M3 = Mesh.TensorMesh([hxind, hyind, hzind], "CCC")
+    indxd, indxu, indyd, indyu, indzd, indzu = M3.faceBoundaryInd
+    mu0 = 4*np.pi*1e-7
+    chibkg = 0.
+    chiblk = 0.01
+    chi = np.ones(M3.nC)*chibkg
+    sph_ind = spheremodel(M3, 0, 0, 0, 100)
+    chi[sph_ind] = chiblk
+    mu = (1.+chi)*mu0
+    Bbc, const = CongruousMagBC(M3, np.array([1., 0., 0.]), chi)
+
+    flag = 'secondary'
+    Box = 1.
+    H0 = Box/mu_0
+    Bbcxx, Bbcxy, Bbcxz  = MagSphereAnaFun(M3.gridFx[(indxd|indxu),0], M3.gridFx[(indxd|indxu),1], M3.gridFx[(indxd|indxu),2], 100, 0., 0., 0., mu_0, mu_0*(1+chiblk), H0, flag)
+    Bbcyx, Bbcyy, Bbcyz  = MagSphereAnaFun(M3.gridFy[(indyd|indyu),0], M3.gridFy[(indyd|indyu),1], M3.gridFy[(indyd|indyu),2], 100, 0., 0., 0., mu_0, mu_0*(1+chiblk), H0, flag)
+    Bbczx, Bbczy, Bbczz  = MagSphereAnaFun(M3.gridFz[(indzd|indzu),0], M3.gridFz[(indzd|indzu),1], M3.gridFz[(indzd|indzu),2], 100, 0., 0., 0., mu_0, mu_0*(1+chiblk), H0, flag)
+    Bbc_ana = np.r_[Bbcxx, Bbcyy, Bbczz]
+
+    # fig, ax = plt.subplots(1,1, figsize = (10, 10))
+    # ax.plot(Bbc_ana)
+    # ax.plot(Bbc)
+    # plt.show()
+    err = np.linalg.norm(Bbc-Bbc_ana)/np.linalg.norm(Bbc_ana)
+
+    if err < 0.1:
+        print 'Mag Boundary computation is valid, err = ', err
+    else:
+        print 'Mag Boundary computation is wrong!!, err = ', err
+    pass

SimPEG/PF/MagneticsDriver.py

@@ -0,0 +1,334 @@
+import re, os
+from SimPEG import Mesh, np, Utils
+import BaseMag, Magnetics
+
+class MagneticsDriver_Inv(object):
+    """docstring for MagneticsDriver_Inv"""
+
+    def __init__(self, input_file=None):
+        if input_file is not None:
+            self.basePath = os.path.sep.join(input_file.split(os.path.sep)[:-1])
+            if len(self.basePath) > 0:
+                self.basePath += os.path.sep
+            self.readDriverFile(input_file.split(os.path.sep)[-1])
+
+
+    def readDriverFile(self, input_file):
+        """
+            Read input files for forward modeling MAG data with integral form
+            INPUT:
+            input_file: File name containing the forward parameter
+
+            OUTPUT:
+            mshfile
+            obsfile
+            topofile
+            start model
+            ref model
+            mag model
+            weightfile
+            chi_target
+            as, ax ,ay, az
+            upper, lower bounds
+            lp, lqx, lqy, lqz
+
+            # All files should be in the working directory, otherwise the path must
+            # be specified.
+
+        """
+
+
+        fid = open(self.basePath + input_file,'r')
+
+        # Line 1
+        line = fid.readline()
+        l_input  = line.split('!')
+        mshfile = l_input[0].rstrip()
+
+        # Line 2
+        line = fid.readline()
+        l_input  = line.split('!')
+        obsfile = l_input[0].rstrip()
+
+        # Line 3
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input=='null':
+            topofile = []
+
+        else:
+            topofile = l_input[0].rstrip()
+
+
+        # Line 4
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input[0]=='VALUE':
+            mstart = float(l_input[1])
+
+        else:
+            mstart = l_input[0].rstrip()
+
+        # Line 5
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input[0]=='VALUE':
+            mref = float(l_input[1])
+
+        else:
+            mref = l_input[0].rstrip()
+
+        # Line 6
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input[0]=='VALUE':
+            staticInput = float(l_input[1])
+
+        elif l_input[0]=='DEFAULT':
+            staticInput = None
+
+        else:
+            staticInput = l_input[0].rstrip()
+
+
+        # Line 7
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input=='DEFAULT':
+            magfile = []
+
+        else:
+            magfile = l_input[0].rstrip()
+
+        # Line 8
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input=='DEFAULT':
+            wgtfile = []
+
+        else:
+            wgtfile = l_input[0].rstrip()
+
+        # Line 9
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        chi = float(l_input[0])
+
+        # Line 10
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        val = np.array(l_input[0:4])
+        alphas = val.astype(np.float)
+
+        # Line 11
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input[0]=='VALUE':
+            val   = np.array(l_input[1:3])
+            bounds = val.astype(np.float)
+
+        else:
+            bounds = l_input[0].rstrip()
+
+        # Line 12
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input[0]=='VALUE':
+            val   = np.array(l_input[1:6])
+            lpnorms = val.astype(np.float)
+
+        else:
+            lpnorms = l_input[0].rstrip()
+
+        # Line 13
+        line = fid.readline()
+        l_input = re.split('[!\s]',line)
+        if l_input[0]=='VALUE':
+            val   = np.array(l_input[1:3])
+            eps = val.astype(np.float)
+
+        else:
+            eps = [None,None]
+
+        self.mshfile  = mshfile
+        self.obsfile  = obsfile
+        self.topofile = topofile
+        self.mstart   = mstart
+        self._mrefInput = mref
+        self._staticInput = staticInput
+        self.magfile  = magfile
+        self.wgtfile  = wgtfile
+        self.chi      = chi
+        self.alphas   = alphas
+        self.bounds   = bounds
+        self.lpnorms  = lpnorms
+        self.eps      = eps
+
+    @property
+    def mesh(self):
+        if getattr(self, '_mesh', None) is None:
+            self._mesh = Mesh.TensorMesh.readUBC(self.basePath + self.mshfile)
+        return self._mesh
+
+    @property
+    def survey(self):
+        if getattr(self, '_survey', None) is None:
+            self._survey = self.readMagneticsObservations(self.obsfile)
+        return self._survey
+
+    @property
+    def activeCells(self):
+        if getattr(self, '_activeCells', None) is None:
+            if self.topofile == 'null':
+                self._activeCells = np.arange(self.mesh.nC)
+            else:
+                topo = np.genfromtxt(self.basePath + self.topofile, skip_header=1)
+                # Find the active cells
+                active = Utils.surface2ind_topo(self.mesh,topo,'N')
+                inds = np.asarray([inds for inds, elem in enumerate(active, 1) if elem], dtype = int) - 1
+                self._activeCells = inds
+
+        return self._activeCells
+
+    @property
+    def staticCells(self):
+        if getattr(self, '_staticCells', None) is None:
+
+            if getattr(self, '_staticInput', None) is None:
+                # All cells are dynamic: 1's
+                self._dynamicCells = np.arange(len(self.m0))
+                self._staticCells = []
+
+            # Cells with specific value are static: 0's
+            else:
+                if isinstance(self._staticInput, float):
+                    staticCells = self.m0 == self._staticInput
+
+                else:
+                    # Read from file active cells with 0:air, 1:dynamic, -1 static
+                    staticCells = Mesh.TensorMesh.readModelUBC(self.mesh, self.basePath + self._staticInput)
+                    staticCells = staticCells[self.activeCells] == -1
+
+                inds = np.asarray([inds for inds, elem in enumerate(staticCells, 1) if elem], dtype = int) - 1
+                self._staticCells = inds
+
+        return self._staticCells
+
+    @property
+    def dynamicCells(self):
+        if getattr(self, '_dynamicCells', None) is None:
+
+            if getattr(self, '_staticInput', None) is None:
+                # All cells are dynamic: 1's
+                self._dynamicCells = np.arange(len(self.m0))
+
+            # Cells with specific value are static: 0's
+            else:
+                if isinstance(self._staticInput, float):
+                    dynamicCells = self.m0 != self._staticInput
+
+                else:
+                    # Read from file active cells with 0:air, 1:dynamic, -1 static
+                    dynamicCells = Mesh.TensorMesh.readModelUBC(self.mesh, self.basePath + self._staticInput)
+                    dynamicCells = dynamicCells[self.activeCells] == 1
+
+                inds = np.asarray([inds for inds, elem in enumerate(dynamicCells, 1) if elem], dtype = int) - 1
+                self._dynamicCells = inds
+
+        return self._dynamicCells
+
+    @property
+    def nC(self):
+        if getattr(self, '_nC', None) is None:
+            self._nC = len(self.activeCells)
+        return self._nC
+
+    @property
+    def m0(self):
+        if getattr(self, '_m0', None) is None:
+            if isinstance(self.mstart, float):
+                self._m0 = np.ones(self.nC) * self.mstart
+            else:
+                self._m0 = Mesh.TensorMesh.readModelUBC(self.mesh,self.basePath + self.mstart)
+                self._m0 = self._m0[self.activeCells]
+
+        return self._m0
+
+    @property
+    def mref(self):
+        if getattr(self, '_mref', None) is None:
+            if isinstance(self._mrefInput, float):
+                self._mref = np.ones(self.nC) * self._mrefInput
+            else:
+                self._mref = Mesh.TensorMesh.readModelUBC(self.mesh,self.basePath + self._mrefInput)
+                self._mref = self._mref[self.activeCells]
+        return self._mref
+
+
+    @property
+    def magnetizationModel(self):
+        """
+            magnetization vector
+        """
+
+        if self.magfile == 'DEFAULT':
+            return Magnetics.dipazm_2_xyz(np.ones(self.nC) * self.survey.srcField.param[1], np.ones(self.nC) * self.survey.srcField.param[2])
+
+        else:
+            raise NotImplementedError("this will require you to read in a three column vector model")
+            self._mref = Utils.meshutils.readUBCTensorModel(self.basePath + self._mrefInput, self.mesh)
+            return np.genfromtxt(self.magfile,delimiter=' \n',dtype=np.str,comments='!')
+
+    def readMagneticsObservations(self, obs_file):
+        """
+            Read and write UBC mag file format
+
+            INPUT:
+            :param fileName, path to the UBC obs mag file
+
+            OUTPUT:
+            :param survey
+            :param M, magnetization orentiaton (MI, MD)
+        """
+
+        fid = open(self.basePath + obs_file,'r')
+
+        # First line has the inclination,declination and amplitude of B0
+        line = fid.readline()
+        B = np.array(line.split(),dtype=float)
+
+        # Second line has the magnetization orientation and a flag
+        line = fid.readline()
+        M = np.array(line.split(),dtype=float)
+
+        # Third line has the number of rows
+        line = fid.readline()
+        ndat = np.array(line.split(),dtype=int)
+
+        # Pre-allocate space for obsx, obsy, obsz, data, uncert
+        line = fid.readline()
+        temp = np.array(line.split(),dtype=float)
+
+        d  = np.zeros(ndat, dtype=float)
+        wd = np.zeros(ndat, dtype=float)
+        locXYZ = np.zeros( (ndat,3), dtype=float)
+
+        for ii in range(ndat):
+
+            temp = np.array(line.split(),dtype=float)
+            locXYZ[ii,:] = temp[:3]
+
+            if len(temp) > 3:
+                d[ii] = temp[3]
+
+                if len(temp)==5:
+                    wd[ii] = temp[4]
+
+            line = fid.readline()
+
+        rxLoc = BaseMag.RxObs(locXYZ)
+        srcField = BaseMag.SrcField([rxLoc],param=(B[2],B[0],B[1]))
+        survey = BaseMag.LinearSurvey(srcField)
+        survey.dobs =  d
+        survey.std =  wd
+        return survey

SimPEG/PF/__init__.py

@@ -0,0 +1,7 @@
+import MagAnalytics
+import BaseMag
+import Magnetics
+import BaseGrav
+import Gravity
+import MagneticsDriver
+import GravityDriver

docs/conf.py

@@ -289,4 +289,6 @@ nitpick_ignore = [
     ('py:class', 'SurveyDC'),
     ('py:class', 'BaseMTFields'),
     ('py:class', 'SolverLU'),
+    ('py:class', 'BaseMagSurvey'),
+    ('py:class', 'BaseMagMap'),
 ]

docs/content/examples/Inversion_IRLS.rst

@@ -0,0 +1,26 @@
+.. _examples_Inversion_IRLS:
+
+.. --------------------------------- ..
+..                                   ..
+..    THIS FILE IS AUTO GENEREATED   ..
+..                                   ..
+..    SimPEG/Examples/__init__.py    ..
+..                                   ..
+.. --------------------------------- ..
+
+
+Inversion: Linear Problem
+=========================
+
+Here we go over the basics of creating a linear problem and inversion.
+
+
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.Inversion_IRLS.run()
+
+.. literalinclude:: ../../../SimPEG/Examples/Inversion_IRLS.py
+    :language: python
+    :linenos:

docs/content/examples/PF_Magnetics_Analytics.rst

@@ -0,0 +1,26 @@
+.. _examples_PF_Magnetics_Analytics:
+
+.. --------------------------------- ..
+..                                   ..
+..    THIS FILE IS AUTO GENEREATED   ..
+..                                   ..
+..    SimPEG/Examples/__init__.py    ..
+..                                   ..
+.. --------------------------------- ..
+
+
+PF: Magnetics: Analytics
+========================
+
+Comparing the magnetics field in Vancouver to Seoul
+
+
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.PF_Magnetics_Analytics.run()
+
+.. literalinclude:: ../../../SimPEG/Examples/PF_Magnetics_Analytics.py
+    :language: python
+    :linenos:

docs/content/pf/index.rst

@@ -0,0 +1,170 @@
+.. math::
+
+    \renewcommand{\div}{\nabla\cdot\,}
+    \newcommand{\grad}{\vec \nabla}
+    \newcommand{\curl}{{\vec \nabla}\times\,}
+    \newcommand {\J}{{\vec J}}
+    \renewcommand{\H}{{\vec H}}
+    \newcommand {\E}{{\vec E}}
+    \newcommand{\dcurl}{{\mathbf C}}
+    \newcommand{\dgrad}{{\mathbf G}}
+    \newcommand{\Acf}{{\mathbf A_c^f}}
+    \newcommand{\Ace}{{\mathbf A_c^e}}
+    \renewcommand{\S}{{\mathbf \Sigma}}
+    \renewcommand{\Div}{{\mathbf {Div}}}
+    \newcommand{\St}{{\mathbf \Sigma_\tau}}
+    \newcommand{\T}{{\mathbf T}}
+    \newcommand{\Tt}{{\mathbf T_\tau}}
+    \newcommand{\diag}{\mathbf{diag}}
+    \newcommand{\M}{{\mathbf M}}
+    \newcommand{\MfMui}{{\M^f_{\mu^{-1}}}}
+    \newcommand{\dMfMuI}{{d_m (\M^f_{\mu^{-1}})^{-1}}}
+    \newcommand{\MeSig}{{\M^e_\sigma}}
+    \newcommand{\MeSigInf}{{\M^e_{\sigma_\infty}}}
+    \newcommand{\MeSigO}{{\M^e_{\sigma_0}}}
+    \newcommand{\Me}{{\M^e}}
+    \newcommand{\Mes}[1]{{\M^e_{#1}}}
+    \newcommand{\Mee}{{\M^e_e}}
+    \newcommand{\Mej}{{\M^e_j}}
+    \newcommand{\BigO}[1]{\mathcal{O}\bigl(#1\bigr)}
+    \newcommand{\bE}{\mathbf{E}}
+    \newcommand{\bH}{\mathbf{H}}
+    \newcommand{\B}{\vec{B}}
+    \newcommand{\D}{\vec{D}}
+    \renewcommand{\H}{\vec{H}}
+    \newcommand{\s}{\vec{s}}
+    \newcommand{\bfJ}{\bf{J}}
+    \newcommand{\vecm}{\vec m}
+    \renewcommand{\Re}{\mathsf{Re}}
+    \renewcommand{\Im}{\mathsf{Im}}
+    \renewcommand {\j}  { {\vec j} }
+    \newcommand {\h}  { {\vec h} }
+    \renewcommand {\b}  { {\vec b} }
+    \newcommand {\e}  { {\vec e} }
+    \newcommand {\c}  { {\vec c} }
+    \renewcommand {\d}  { {\vec d} }
+    \renewcommand {\u}  { {\vec u} }
+    \newcommand{\I}{\vec{I}}
+
+Magnetics
+*********
+
+
+The geomagnetic field can be ranked as the longest studied of all the geophysical properties of the earth. In addition, magnetic survey, has been used broadly in diverse realm e.g., mining, oil and gas industry and environmental engineering. Although, this geophysical application is quite common in geoscience; however, we do not have modular, well-documented and well-tested open-source codes, which perform forward and inverse problems of magnetic survey. Therefore, here we are going to build up magnetic forward and inverse modeling code based on  two common methodologies for forward problem - differential equation and integral equation approaches. \
+
+First, we start with some backgrounds of magnetics, e.g., Maxwell's equations. Based on that secondly, we use differential equation approach to solve forward problem with secondary field formulation. In order to discretzie our system here, we use finite volume approach with weak formulation. Third, we solve inverse problem through Gauss-Newton method.
+
+Backgrounds
+===========
+Maxwell's equations for static case with out current source can be written as
+
+.. math::
+
+    \nabla U = \frac{1}{\mu}\vec{B} \\
+
+    \nabla \cdot \vec{B} = 0
+
+where \\(\\vec{B}\\) is magnetic flux (\\(\T\\)) and \\(\U\\) is magnetic potential and \\(\\mu\\) is permeability. Since we do not have any source term in above equations, boundary condition is going to be the driving force of our system as given below
+
+.. math::
+
+    (\vec{B}\cdot{\vec{n}})_{\partial\Omega} = B_{BC}
+
+where \\(\\vec{n}\\) means the unit normal vector on the boundary surface (\\(\\partial \\Omega\\)). By using seocondary field formulation we can rewrite above equations as
+
+.. math::
+
+    \frac{1}{\mu}\vec{B}_s = (\frac{1}{\mu}_0-\frac{1}{\mu})\vec{B}_0+\nabla\phi_s
+
+    \nabla \cdot \vec{B}_s = 0
+
+    (\vec{B}_s\cdot{\vec{n}})_{\partial\Omega} = B_{sBC}
+
+where \\(\\vec{B}_s\\) is the secondary magnetic flux and \\(\\vec{B}_0\\) is the background or primary magnetic flux. In practice, we consider our earth field, which we can get from International Geomagnetic Reference Field (IGRF) by specifying the time and location, as  \\(\\vec{B}_0\\). And based on this background fields, we compute secondary fields (\\(\\vec{B}_s\\)). Now we introduce the susceptibility as
+
+.. math::
+
+    \chi = \frac{\mu}{\mu_0} - 1 \\
+
+    \mu = \mu_0(1+\chi)
+
+Since most materials in the earth  have lower permeability than \\(\\mu_0\\), usually \\(\\chi\\) is greater than 0.
+
+.. note::
+
+    Actually, this is an assumption, which means we are not sure exactly this is true, although we are sure, it is very rare that we can encounter those materials. Anyway, practical range of the susceptibility is \\(0 < \\chi < 1 \\).
+
+Since we compute secondary field based on the earth field, which can be different from different locations in the world, we can expect different anomalous responses in different locations in the earth. For instance, assume we have two susceptible spheres, which are exactly same. However, anomalous responses in Seoul and Vancouver are going to be different.
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.PF_Magnetics_Analytics.run()
+
+Since we can measure total fields ( \\(\\vec{B}\\)), and usually have reasonably accurate earth field (\\(\\vec{B}_0\\)), we can compute anomalous fields, \\(\\vec{B}_s\\) from our observed data. If you want to download earth magnetic fields at specific location see this website (`noaa <http://www.ngdc.noaa.gov/geomag-web/>`_).
+
+What is our data?
+-----------------
+
+In applied geophysics, which means in practice, it is common to refer to measurements as "the magnetic anomaly" and we can consider this as our observed data. For further descriptions in `GPG <http://www.eos.ubc.ca/courses/eosc350/content/>`_ materials for magnetic survey. Now we have the simple relation ship between "the magnetic anomaly" and the total field as
+
+.. math::
+
+	\triangle\vec{B} = |\hat{B}_o-\vec{B}_s|-|\hat{B}_o| \approx |\vec{B}_s|cos \theta
+
+where \\(\\theta\\) is the angle between total and anomalous fields, \\(\\hat{B}_o\\) is the unit vector for \\(\\vec{B}_o\\). Equivalently, we can use the vector dot product to show that the anomalous field is approximately equal to the projection of that field onto the direction of the inducing field. Using this approach we would write
+
+.. math::
+
+	\triangle\vec{B} = |\vec{B}_s|cos \theta = |\hat{B}_o||\vec{B}_s|cos \theta = \hat{B}_o \cdot \vec{B}_s
+
+This is important because, in practice we usually use a total field magnetometer (like a proton precession or optically pumped sensor), which can measure only that part of the anomalous field which is in the direction of the earth's main field.
+
+Sphere in a whole space
+-----------------------
+
+
+Forward problem
+===============
+
+Differential equation approach
+------------------------------
+
+    .. math::
+
+        \mathbf{A}\mathbf{u} = \mathbf{rhs}
+
+        \mathbf{A} =  \Div(\MfMui)^{-1}\Div^{T}
+
+        \mathbf{rhs} =  \Div(\MfMui)^{-1}\mathbf{M}^f_{\mu_0^{-1}}\mathbf{B}_0 - \Div\mathbf{B}_0+\diag(v)\mathbf{D} \mathbf{P}_{out}^T \mathbf{B}_{sBC}
+
+        \mathbf{B}_s = (\MfMui)^{-1}\mathbf{M}^f_{\mu_0^{-1}}\mathbf{B}_0-\mathbf{B}_0 -(\MfMui)^{-1}\Div^T \mathbf{u}
+
+
+Mag Differential eq. approach
+*****************************
+
+.. autoclass:: SimPEG.PF.Magnetics.Problem3D_DiffSecondary
+    :show-inheritance:
+    :members:
+    :undoc-members:
+    :inherited-members:
+
+.. autoclass:: SimPEG.PF.BaseMag.BaseMagSurvey
+    :show-inheritance:
+    :members:
+    :undoc-members:
+    :inherited-members:
+
+
+Mag Integral eq. approach
+*************************
+
+Mag analytic solutions
+**********************
+
+.. automodule:: SimPEG.PF.MagAnalytics
+    :show-inheritance:
+    :members:
+    :undoc-members:
+    :inherited-members:

docs/index.rst

@@ -62,6 +62,7 @@ Packages
    content/dc/index
    content/ip/index
    content/mt/index
+   content/pf/index
    content/flow/index
 
 Finite Volume

tests/flow/test_Richards.py

@@ -14,6 +14,7 @@ TOL = 1E-8
 
 np.random.seed(0)
 
+
 class TestModels(unittest.TestCase):
 
     def test_BaseHaverkamp_Theta(self):

tests/pf/__init__.py

@@ -0,0 +1,12 @@
+import os
+import glob
+import unittest
+
+if __name__ == '__main__':
+    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)
+
+    unittest.TextTestRunner(verbosity=2).run(testSuite)

tests/pf/assets/magnetics/Mesh_10m.msh

@@ -0,0 +1,5 @@
+47 47 20
+-60.00 -60.00 280.00
+50.00 30.00 20.00 41*10.00 20.00 30.00 50.00 
+50.00 30.00 20.00 41*10.00 20.00 30.00 50.00 
+17*10.00 20.00 30.00 50

tests/pf/assets/magnetics/Obs_loc_TMI.obs

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tests/pf/assets/magnetics/PYMAG3D_inv.inp

@@ -0,0 +1,13 @@
+Mesh_10m.msh			! Mesh file
+Obs_loc_TMI.obs			! Obsfile
+Gaussian.topo			! Topofile | null
+ModelStart.sus			! Starting model
+VALUE 0				! Reference model
+ActiveCells.dat			! [ Active file (0:Inactive | 1: Active-Dynamic | -1: Active-Static) ] || [ VALUE ### (from starting model) ] || [ DEFAULT (all Active-Dynamic)]
+DEFAULT !..\AzmDip.dat		! Magnetization vector model
+DEFAULT				! Cell based weight file
+1				! target chi factor | DEFAULT=1
+1 1 1 1				! alpha s, x ,y ,z
+VALUE 0 1			! Lower and Upper Bounds for p-component
+VALUE 0 1 1 1 1			! lp-norm for amplitude inversion FILE pqxqyqzr.dat  ! Norms VALUE p, qx, qy, qz, r | FILE m-by-5 matrix
+DEFAULT		! Threshold value for the norm on model and model gradient VALUE eps_p, eps_q | DEFAULT

tests/pf/test_forward_PFproblem.py

@@ -0,0 +1,56 @@
+import unittest
+from SimPEG import Mesh, Utils, np, PF
+import matplotlib.pyplot as plt
+
+
+class MagFwdProblemTests(unittest.TestCase):
+
+    def setUp(self):
+
+        cs = 25.
+        hxind = [(cs, 5, -1.3), (cs/2.0, 41), (cs, 5, 1.3)]
+        hyind = [(cs, 5, -1.3), (cs/2.0, 41), (cs, 5, 1.3)]
+        hzind = [(cs, 5, -1.3), (cs/2.0, 40), (cs, 5, 1.3)]
+        M = Mesh.TensorMesh([hxind, hyind, hzind], 'CCC')
+
+        chibkg = 0.
+        chiblk = 0.01
+        chi = np.ones(M.nC)*chibkg
+        sph_ind = PF.MagAnalytics.spheremodel(M, 0., 0., 0., 100)
+        chi[sph_ind] = chiblk
+        model = PF.BaseMag.BaseMagMap(M)
+        prob = PF.Magnetics.Problem3D_DiffSecondary(M, mapping=model)
+        self.prob = prob
+        self.M = M
+        self.chi = chi
+
+    def test_ana_forward(self):
+
+        survey = PF.BaseMag.BaseMagSurvey()
+
+        Inc = 45.
+        Dec = 45.
+        Btot = 51000
+
+        b0 = PF.MagAnalytics.IDTtoxyz(Inc, Dec, Btot)
+        survey.setBackgroundField(Inc, Dec, Btot)
+        xr = np.linspace(-300, 300, 41)
+        yr = np.linspace(-300, 300, 41)
+        X, Y = np.meshgrid(xr, yr)
+        Z = np.ones((xr.size, yr.size))*150
+        rxLoc = np.c_[Utils.mkvc(X), Utils.mkvc(Y), Utils.mkvc(Z)]
+        survey.rxLoc = rxLoc
+
+        self.prob.pair(survey)
+        u = self.prob.fields(self.chi)
+        B = u['B']
+
+        bxa, bya, bza = PF.MagAnalytics.MagSphereAnaFunA(rxLoc[:, 0], rxLoc[:, 1], rxLoc[:, 2], 100., 0., 0., 0., 0.01, b0, 'secondary')
+
+        dpred = survey.projectFieldsAsVector(B)
+        err = np.linalg.norm(dpred-np.r_[bxa, bya, bza])/np.linalg.norm(np.r_[bxa, bya, bza])
+        self.assertTrue(err < 0.08)
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/pf/test_magnetics_IO.py

@@ -0,0 +1,33 @@
+import unittest
+from SimPEG import Mesh, np, PF
+from scipy.constants import mu_0
+import os
+
+
+class MagSensProblemTests(unittest.TestCase):
+
+    def setUp(self):
+        pass
+
+    def test_magnetics_inversion(self):
+
+        driver = PF.MagneticsDriver.MagneticsDriver_Inv(
+            os.path.sep.join(['assets', 'magnetics', 'PYMAG3D_inv.inp'])
+        )
+
+        print driver.mesh
+        print driver.survey
+        print driver.m0
+        print driver.mref
+        print driver.activeCells
+        print driver.staticCells
+        print driver.dynamicCells
+        print driver.chi
+        print driver.nC
+        print driver.alphas
+        print driver.bounds
+        print driver.lpnorms
+        print driver.eps
+
+if __name__ == '__main__':
+    unittest.main()

tests/pf/test_magnetics_analytics.py

@@ -0,0 +1,48 @@
+import unittest
+from SimPEG import Mesh, np, PF
+from scipy.constants import mu_0
+
+
+plotIt = False
+
+
+class TestBoundaryConditionAnalytics(unittest.TestCase):
+
+    def test_ana_boundary_computation(self):
+
+        hxind = [(0, 25, 1.3), (21, 12.5), (0, 25, 1.3)]
+        hyind = [(0, 25, 1.3), (21, 12.5), (0, 25, 1.3)]
+        hzind = [(0, 25, 1.3), (20, 12.5), (0, 25, 1.3)]
+        # hx, hy, hz = Utils.meshTensors(hxind, hyind, hzind)
+        M3 = Mesh.TensorMesh([hxind, hyind, hzind], "CCC")
+        indxd, indxu, indyd, indyu, indzd, indzu = M3.faceBoundaryInd
+        mu0 = 4*np.pi*1e-7
+        chibkg = 0.
+        chiblk = 0.01
+        chi = np.ones(M3.nC)*chibkg
+        sph_ind = PF.MagAnalytics.spheremodel(M3, 0, 0, 0, 100)
+        chi[sph_ind] = chiblk
+        mu = (1.+chi)*mu0
+        Bbc, const = PF.MagAnalytics.CongruousMagBC(M3, np.array([1., 0., 0.]), chi)
+
+        flag = 'secondary'
+        Box = 1.
+        H0 = Box/mu_0
+        Bbcxx, Bbcxy, Bbcxz  = PF.MagAnalytics.MagSphereAnaFun(M3.gridFx[(indxd|indxu),0], M3.gridFx[(indxd|indxu),1], M3.gridFx[(indxd|indxu),2], 100, 0., 0., 0., mu_0, mu_0*(1+chiblk), H0, flag)
+        Bbcyx, Bbcyy, Bbcyz  = PF.MagAnalytics.MagSphereAnaFun(M3.gridFy[(indyd|indyu),0], M3.gridFy[(indyd|indyu),1], M3.gridFy[(indyd|indyu),2], 100, 0., 0., 0., mu_0, mu_0*(1+chiblk), H0, flag)
+        Bbczx, Bbczy, Bbczz  = PF.MagAnalytics.MagSphereAnaFun(M3.gridFz[(indzd|indzu),0], M3.gridFz[(indzd|indzu),1], M3.gridFz[(indzd|indzu),2], 100, 0., 0., 0., mu_0, mu_0*(1+chiblk), H0, flag)
+        Bbc_ana = np.r_[Bbcxx, Bbcyy, Bbczz]
+
+        if plotIt:
+            import matplotlib.pyplot as plt
+            fig, ax = plt.subplots(1,1, figsize = (10, 10))
+            ax.plot(Bbc_ana)
+            ax.plot(Bbc)
+            plt.show()
+        err = np.linalg.norm(Bbc-Bbc_ana) / np.linalg.norm(Bbc_ana)
+
+        assert err < 0.1, 'Mag Boundary computation is wrong!!, err = {}'.format(err)
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/pf/test_sensitivity_PFproblem.py

@@ -0,0 +1,306 @@
+# import unittest
+# from SimPEG import *
+# from simpegPF import BaseMag
+# import matplotlib.pyplot as plt
+# import simpegPF as PF
+# from scipy.constants import mu_0
+
+
+# class MagSensProblemTests(unittest.TestCase):
+
+#     def setUp(self):
+#         cs = 25.
+#         hxind = [(cs, 5, -1.3), (cs, 21), (cs, 5, 1.3)]
+#         hyind = [(cs, 5, -1.3), (cs, 21), (cs, 5, 1.3)]
+#         hzind = [(cs, 5, -1.3), (cs, 20), (cs, 5, 1.3)]
+#         M = Mesh.TensorMesh([hxind, hyind, hzind], 'CCC')
+#         chibkg = 0.001
+#         chiblk = 0.01
+#         chi = np.ones(M.nC)*chibkg
+
+#         Inc = 90.
+#         Dec = 0.
+#         Btot = 51000
+
+#         b0 = PF.MagAnalytics.IDTtoxyz(Inc, Dec, Btot)
+#         sph_ind = PF.MagAnalytics.spheremodel(M, 0., 0., 0., 100)
+#         chi[sph_ind] = chiblk
+#         model = PF.BaseMag.BaseMagMap(M)
+
+#         survey = BaseMag.BaseMagSurvey()
+
+#         survey.setBackgroundField(Inc, Dec, Btot)
+#         xr = np.linspace(-300, 300, 41)
+#         yr = np.linspace(-300, 300, 41)
+#         X, Y = np.meshgrid(xr, yr)
+#         Z = np.ones((xr.size, yr.size))*150
+#         rxLoc = np.c_[Utils.mkvc(X), Utils.mkvc(Y), Utils.mkvc(Z)]
+#         survey.rxLoc = rxLoc
+
+#         prob = PF.Magnetics.Problem3D_DiffSecondary(M, mapping=model)
+#         prob.pair(survey)
+#         dpre = survey.dpred(chi)
+
+#         fields = prob.fields(chi)
+#         self.u = fields['u']
+#         self.B = fields['B']
+
+#         self.survey = survey
+#         self.model = model
+#         self.prob = prob
+#         self.M = M
+#         self.chi = chi
+
+#     def test_mass(self):
+#         print '\n >>Derivative for MfMuI works.'
+#         mu = self.model*self.chi
+
+#         def MfmuI(mu):
+
+#             chi = mu/mu_0-1
+#             self.prob.makeMassMatrices(chi)
+#             vol = self.prob.mesh.vol
+#             aveF2CC = self.prob.mesh.aveF2CC
+#             MfMuI = self.prob.MfMuI.diagonal()
+
+#             return MfMuI
+
+#         def dMfmuI(mu, v):
+
+#             chi = mu/mu_0-1
+#             self.prob.makeMassMatrices(chi)
+#             vol = self.prob.mesh.vol
+#             aveF2CC = self.prob.mesh.aveF2CC
+#             MfMuI = self.prob.MfMuI.diagonal()
+#             dMfMuI = Utils.sdiag(MfMuI**2)*aveF2CC.T*Utils.sdiag(vol*1./mu**2)
+
+#             return dMfMuI*v
+
+#         d_mu = mu*0.8
+#         derChk = lambda m: [MfmuI(m), lambda mx: dMfmuI(self.chi, mx)]
+#         passed = Tests.checkDerivative(derChk, mu, num=4, dx = d_mu, plotIt=False)
+
+#         self.assertTrue(passed)
+
+
+#     def test_dCdm_Av(self):
+#         print '\n >>Derivative for Cm_A.'
+#         Div = self.prob._Div
+#         vol = self.prob.mesh.vol
+#         aveF2CC = self.prob.mesh.aveF2CC
+
+#         def Cm_A(chi):
+#             dmudm = self.model.deriv(chi)
+#             u = self.u
+#             # chi = mu/mu_0-1
+#             self.prob.makeMassMatrices(chi)
+#             mu = self.model*(self.chi)
+#             A = self.prob.getA(self.chi)
+#             MfMuIvec = 1/self.prob.MfMui.diagonal()
+#             dMfMuI = Utils.sdiag(MfMuIvec**2)*aveF2CC.T*Utils.sdiag(vol*1./mu**2)
+
+#             Cm_A =  A*u
+
+#             return Cm_A
+
+#         def dCdm_A(chi, v):
+
+#             dmudm = self.model.deriv(chi)
+#             u = self.u
+#             self.prob.makeMassMatrices(chi)
+#             mu = self.model*self.chi
+#             A = self.prob.getA(self.chi)
+#             MfMuIvec = 1/self.prob.MfMui.diagonal()
+#             dMfMuI = Utils.sdiag(MfMuIvec**2)*aveF2CC.T*Utils.sdiag(vol*1./mu**2)
+
+#             Cm_A =  A*u
+#             dCdm_A = Div * (Utils.sdiag( Div.T * u ) * dMfMuI * dmudm)
+
+#             return dCdm_A*v
+
+#         d_chi = self.chi*0.8
+#         derChk = lambda m: [Cm_A(m), lambda mx: dCdm_A(self.chi, mx)]
+#         passed = Tests.checkDerivative(derChk, self.chi, num=4, dx = d_chi, plotIt=False)
+#         self.assertTrue(passed)
+
+
+#     def test_dCdmu_RHS(self):
+#         print '\n >>Derivative for Cm_RHS.'
+#         u = self.u
+#         Div = self.prob._Div
+#         mu = self.model*self.chi
+#         vol = self.prob.mesh.vol
+#         Mc = Utils.sdiag(vol)
+#         aveF2CC = self.prob.mesh.aveF2CC
+#         B0 = self.prob.getB0()
+#         Dface = self.prob.mesh.faceDiv
+
+#         def Cm_RHS(chi):
+
+#             self.prob.makeMassMatrices(chi)
+#             dmudm = self.model.deriv(chi)
+#             dchidmu = Utils.sdiag(1/(dmudm.diagonal()))
+#             Bbc, Bbc_const = PF.MagAnalytics.CongruousMagBC(self.prob.mesh, self.survey.B0, chi)
+#             MfMuIvec = 1/self.prob.MfMui.diagonal()
+#             dMfMuI = Utils.sdiag(MfMuIvec**2)*aveF2CC.T*Utils.sdiag(vol*1./mu**2)
+#             RHS1 = Div*self.prob.MfMuI*self.prob.MfMu0*B0
+#             RHS2 =  Mc*Dface*self.prob._Pout.T*Bbc
+#             RHS = RHS1 + RHS2 + Div*B0
+
+#             return RHS
+
+
+#         def dCdm_RHS(chi, v):
+
+
+#             self.prob.makeMassMatrices(chi)
+#             dmudm = self.model.deriv(chi)
+#             dmdmu = Utils.sdiag(1/(dmudm.diagonal()))
+#             Bbc, Bbc_const = PF.MagAnalytics.CongruousMagBC(self.prob.mesh, self.survey.B0, chi)
+#             MfMuIvec = 1/self.prob.MfMui.diagonal()
+#             dMfMuI = Utils.sdiag(MfMuIvec**2)*aveF2CC.T*Utils.sdiag(vol*1./mu**2)
+#             dCdm_RHS1 = Div * (Utils.sdiag( self.prob.MfMu0*B0  ) * dMfMuI)
+#             temp1 = (Dface*(self.prob._Pout.T*Bbc_const*Bbc))
+#             dCdm_RHS2v  = (Utils.sdiag(vol)*temp1)*np.inner(vol, v)
+#             dCdm_RHSv =  dCdm_RHS1*(dmudm*v) + dCdm_RHS2v
+
+#             return dCdm_RHSv
+
+#         d_chi = self.chi*0.8
+#         derChk = lambda m: [Cm_RHS(m), lambda mx: dCdm_RHS(self.chi, mx)]
+#         passed = Tests.checkDerivative(derChk, self.chi, num=4, dx = d_chi, plotIt=False)
+#         self.assertTrue(passed)
+
+
+#     # def test_dudm(self):
+#     #     print ">> Derivative test for dudm"
+#     #     u = self.u
+#     #     Div = self.prob._Div
+#     #     mu = self.model*(self.chi)
+#     #     vol = self.prob.mesh.vol
+#     #     Mc = Utils.sdiag(vol)
+#     #     aveF2CC = self.prob.mesh.aveF2CC
+#     #     B0 = self.prob.getB0()
+#     #     Dface = self.prob.mesh.faceDiv
+
+#     #     def ufun(chi):
+#     #         u = self.prob.fields(chi)['u']
+#     #         return u
+
+#     #     def dudm(chi, v):
+
+#     #         chi = mu/mu_0-1
+#     #         self.prob.makeMassMatrices(chi)
+#     #         u = self.u
+#     #         dmudm = self.model.deriv(chi)
+#     #         dmdmu = Utils.sdiag(1/(dmudm.diagonal()))
+#     #         Bbc, Bbc_const = PF.MagAnalytics.CongruousMagBC(self.prob.mesh, self.survey.B0, chi)
+#     #         MfMuIvec = 1/self.prob.MfMui.diagonal()
+#     #         dMfMuI = Utils.sdiag(MfMuIvec**2)*aveF2CC.T*Utils.sdiag(vol*1./mu**2)
+#     #         dCdu = self.prob.getA(chi)
+#     #         dCdm_A = Div * ( Utils.sdiag( Div.T * u )* dMfMuI *dmudm  )
+#     #         dCdm_RHS1 = Div * (Utils.sdiag( self.prob.MfMu0*B0  ) * dMfMuI)
+#     #         temp1 = (Dface*(self.prob._Pout.T*Bbc_const*Bbc))
+#     #         dCdm_RHS2v  = (Utils.sdiag(vol)*temp1)*np.inner(vol, v)
+#     #         dCdm_RHSv =  dCdm_RHS1*(dmudm*v) +  dCdm_RHS2v
+#     #         dCdm_v = dCdm_A*v - dCdm_RHSv
+#     #         m1 = sp.linalg.interface.aslinearoperator(Utils.sdiag(1/dCdu.diagonal()))
+#     #         sol, info = sp.linalg.bicgstab(dCdu, dCdm_v, tol=1e-8, maxiter=1000, M=m1)
+
+#     #         dudm = -sol
+
+#     #         return dudm
+
+#     #     d_chi = 10.0*self.chi #np.random.rand(mesh.nCz)
+#     #     d_sph_ind = PF.MagAnalytics.spheremodel(self.prob.mesh, 0., 0., -50., 50)
+#     #     d_chi[d_sph_ind] = 0.1
+
+#     #     derChk = lambda m: [ufun(m), lambda mx: dudm(self.chi, mx)]
+#     #     # TODO: I am not sure why the order get worse as step decreases .. --;
+#     #     passed = Tests.checkDerivative(derChk, self.chi, num=2, dx = d_chi, plotIt=False)
+#     #     self.assertTrue(passed)
+
+
+#     # def test_dBdm(self):
+#     #     print ">> Derivative test for dBdm"
+#     #     u = self.u
+#     #     Div = self.prob._Div
+#     #     mu = self.model*(self.chi)
+#     #     vol = self.prob.mesh.vol
+#     #     Mc = Utils.sdiag(vol)
+#     #     aveF2CC = self.prob.mesh.aveF2CC
+#     #     B0 = self.prob.getB0()
+#     #     Dface = self.prob.mesh.faceDiv
+
+#     #     def Bfun(chi):
+#     #         B = self.prob.fields(chi)['B']
+#     #         return B
+
+#     #     def dBdm(chi, v):
+
+#     #         chi = mu/mu_0-1
+#     #         self.prob.makeMassMatrices(chi)
+#     #         u = self.u
+#     #         dmudm = self.model.deriv(chi)
+#     #         dmdmu = Utils.sdiag(1/(dmudm.diagonal()))
+#     #         Bbc, Bbc_const = PF.MagAnalytics.CongruousMagBC(self.prob.mesh, self.survey.B0, chi)
+#     #         MfMuIvec = 1/self.prob.MfMui.diagonal()
+#     #         dMfMuI = Utils.sdiag(MfMuIvec**2)*aveF2CC.T*Utils.sdiag(vol*1./mu**2)
+#     #         dCdu = self.prob.getA(chi)
+#     #         dCdm_A = Div * ( Utils.sdiag( Div.T * u )* dMfMuI *dmudm  )
+#     #         dCdm_RHS1 = Div * (Utils.sdiag( self.prob.MfMu0*B0  ) * dMfMuI)
+#     #         temp1 = (Dface*(self.prob._Pout.T*Bbc_const*Bbc))
+#     #         dCdm_RHS2v  = (Utils.sdiag(vol)*temp1)*np.inner(vol, v)
+#     #         dCdm_RHSv =  dCdm_RHS1*(dmudm*v) +  dCdm_RHS2v
+#     #         dCdm_v = dCdm_A*v - dCdm_RHSv
+#     #         m1 = sp.linalg.interface.aslinearoperator(Utils.sdiag(1/dCdu.diagonal()))
+#     #         sol, info = sp.linalg.bicgstab(dCdu, dCdm_v, tol=1e-8, maxiter=1000, M=m1)
+
+#     #         dudm = -sol
+#     #         dBdmv =       (  Utils.sdiag(self.prob.MfMu0*B0)*(dMfMuI * (dmudm*v)) \
+#     #                      - Utils.sdiag(Div.T*u)*(dMfMuI* (dmudm*v)) \
+#     #                      - self.prob.MfMuI*(Div.T* (dudm)) )
+
+#     #         return dBdmv
+
+#     #     d_chi = 10.0*self.chi #np.random.rand(mesh.nCz)
+#     #     d_sph_ind = PF.MagAnalytics.spheremodel(self.prob.mesh, 0., 0., -50., 50)
+#     #     d_chi[d_sph_ind] = 0.1
+
+#     #     derChk = lambda m: [Bfun(m), lambda mx: dBdm(self.chi, mx)]
+#     #     # TODO: I am not sure why the order get worse as step decreases .. --;
+#     #     passed = Tests.checkDerivative(derChk, self.chi, num=2, dx = d_chi, plotIt=False)
+#     #     self.assertTrue(passed)
+
+
+
+#     def test_Jvec(self):
+#         print ">> Derivative test for Jvec"
+
+#         d_chi = 10.0*self.chi #np.random.rand(mesh.nCz)
+#         d_sph_ind = PF.MagAnalytics.spheremodel(self.prob.mesh, 0., 0., -50., 50)
+#         d_chi[d_sph_ind] = 0.1
+
+#         derChk = lambda m: (self.survey.dpred(m), lambda v: self.prob.Jvec(m, v))
+#         # TODO: I am not sure why the order get worse as step decreases .. --;
+#         passed = Tests.checkDerivative(derChk, self.chi, num=2, dx = d_chi, plotIt=False)
+#         self.assertTrue(passed)
+
+#     def test_Jtvec(self):
+#         print ">> Derivative test for Jtvec"
+#         dobs = self.survey.dpred(self.chi)
+
+#         def misfit(m):
+#             dpre = self.survey.dpred(m)
+#             misfit = 0.5*np.linalg.norm(dpre-dobs)**2
+#             residual = dpre-dobs
+#             dmisfit = self.prob.Jtvec(self.chi, residual)
+
+#             return misfit, dmisfit
+
+#         # TODO: I am not sure why the order get worse as step decreases .. --;
+#         passed = Tests.checkDerivative(misfit, self.chi, num=4, plotIt=False)
+#         self.assertTrue(passed)
+
+# if __name__ == '__main__':
+#     unittest.main()