Problem.Jvec, Problem.Jtvec, Problem.fields, DataMisfit, survey.dpred take a fields object f (not a solution vector, u)

SimPEG/DCIP/BaseDC.py

@@ -200,11 +200,11 @@ class ProblemDC_CC(Problem.BaseProblem):
 
         return F
 
-    def Jvec(self, m, v, u=None):
+    def Jvec(self, m, v, f=None):
         """
             :param numpy.array m: model
             :param numpy.array v: vector to multiply
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: numpy.array
             :return: Jv
 
@@ -225,11 +225,10 @@ class ProblemDC_CC(Problem.BaseProblem):
         # Set current model; clear dependent property $\mathbf{A(m)}$
         self.curModel = m
         sigma = self.curModel.transform # $\sigma = \mathcal{M}(\m)$
-        if u is None:
+        if f is None:
             # Run forward simulation if $u$ not provided
-            u = self.fields(self.curModel)[self.survey.srcList, 'phi_sol']
+            f = self.fields(self.curModel)
-        else:
+        u = f[self.survey.srcList, 'phi_sol']
-            u = u[self.survey.srcList, 'phi_sol']
 
         D = self.mesh.faceDiv
         G = self.mesh.cellGrad
@@ -251,19 +250,18 @@ class ProblemDC_CC(Problem.BaseProblem):
         if self.Ainv is None:
             self.Ainv = self.Solver(dA_du, **self.solverOpts)
 
-        P        = self.survey.getP(self.mesh)
+        P     = self.survey.getP(self.mesh)
         Jv    = - P * mkvc( self.Ainv * dCdm_x_v )
         return Jv
 
-    def Jtvec(self, m, v, u=None):
+    def Jtvec(self, m, v, f=None):
 
         self.curModel = m
         sigma = self.curModel.transform # $\sigma = \mathcal{M}(\m)$
-        if u is None:
+        if f is None:
-            # Run forward simulation if $u$ not provided
+            # Run forward simulation if $f$ not provided
-            u = self.fields(self.curModel)[self.survey.srcList, 'phi_sol']
+            f = self.fields(self.curModel)
-        else:
+        u = f[self.survey.srcList, 'phi_sol']
-            u = u[self.survey.srcList, 'phi_sol']
 
         shp = u.shape
         P = self.survey.getP(self.mesh)

SimPEG/DCIP/BaseIP.py

@@ -14,12 +14,12 @@ class SurveyIP(SurveyDC):
         Survey.BaseSurvey.__init__(self, **kwargs)
         self._Ps = {}
 
-    def dpred(self, m, u=None):
+    def dpred(self, m, f=None):
         """
             Predicted data.
 
             .. math::
-                d_\\text{pred} = Pu(m)
+                d_\\text{pred} = Pf(m)
         """
 
         return self.prob.forward(m)
@@ -143,10 +143,10 @@ class ProblemIP(Problem.BaseProblem):
         J_x_v    = - P * mkvc( self.Ainv * dCdm_x_v )
         return -J_x_v
 
-    def Jvec(self, m, v, u=None):
+    def Jvec(self, m, v, f=None):
         return self.forward(v)
 
-    def Jtvec(self, m, v, u=None):
+    def Jtvec(self, m, v, f=None):
 
         self.curModel = m
         # sigma = self.curModel.transform # $\sigma = \mathcal{M}(\m)$

SimPEG/DataMisfit.py

@@ -22,11 +22,11 @@ class BaseDataMisfit(object):
         Utils.setKwargs(self,**kwargs)
 
     @Utils.timeIt
-    def eval(self, m, u=None):
+    def eval(self, m, f=None):
-        """eval(m, u=None)
+        """eval(m, f=None)
 
             :param numpy.array m: geophysical model
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: float
             :return: data misfit
 
@@ -34,11 +34,11 @@ class BaseDataMisfit(object):
         raise NotImplementedError('This method should be overwritten.')
 
     @Utils.timeIt
-    def evalDeriv(self, m, u=None):
+    def evalDeriv(self, m, f=None):
-        """evalDeriv(m, u=None)
+        """evalDeriv(m, f=None)
 
             :param numpy.array m: geophysical model
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: numpy.array
             :return: data misfit derivative
 
@@ -47,12 +47,12 @@ class BaseDataMisfit(object):
 
 
     @Utils.timeIt
-    def eval2Deriv(self, m, v, u=None):
+    def eval2Deriv(self, m, v, f=None):
-        """eval2Deriv(m, v, u=None)
+        """eval2Deriv(m, v, f=None)
 
             :param numpy.array m: geophysical model
             :param numpy.array v: vector to multiply
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: numpy.array
             :return: data misfit derivative
 
@@ -108,24 +108,20 @@ class l2_DataMisfit(BaseDataMisfit):
         self._Wd = value
 
     @Utils.timeIt
-    def eval(self, m, u=None):
+    def eval(self, m, f=None):
-        "eval(m, u=None)"
+        "eval(m, f=None)"
-        prob   = self.prob
+        if f is None: f = self.prob.fields(m)
-        survey = self.survey
+        R = self.Wd * self.survey.residual(m, f)
-        R = self.Wd * survey.residual(m, u)
         return 0.5*np.vdot(R, R)
 
     @Utils.timeIt
-    def evalDeriv(self, m, u=None):
+    def evalDeriv(self, m, f=None):
-        "evalDeriv(m, u=None)"
+        "evalDeriv(m, f=None)"
-        prob   = self.prob
+        if f is None: f = self.prob.fields(m)
-        survey = self.survey
+        return self.prob.Jtvec(m, self.Wd * (self.Wd * self.survey.residual(m, f=f)), f=f)
-        if u is None: u = prob.fields(m)
-        return prob.Jtvec(m, self.Wd * (self.Wd * survey.residual(m, u)), u)
 
     @Utils.timeIt
-    def eval2Deriv(self, m, v, u=None):
+    def eval2Deriv(self, m, v, f=None):
-        "eval2Deriv(m, v, u=None)"
+        "eval2Deriv(m, v, f=None)"
-        prob   = self.prob
+        if f is None: f = prob.fields(m)
-        if u is None: u = prob.fields(m)
+        return self.prob.Jtvec_approx(m, self.Wd * (self.Wd * prob.Jvec_approx(m, v, f=f)), f=f)
-        return prob.Jtvec_approx(m, self.Wd * (self.Wd * prob.Jvec_approx(m, v, u=u)), u)

SimPEG/FLOW/Richards/RichardsProblem.py

@@ -45,19 +45,19 @@ class RichardsSurvey(Survey.BaseSurvey):
 
     @Utils.count
     @Utils.requires('prob')
-    def dpred(self, m, u=None):
+    def dpred(self, m, f=None):
         """
             Create the projected data from a model.
-            The field, u, (if provided) will be used for the predicted data
+            The field, f, (if provided) will be used for the predicted data
             instead of recalculating the fields (which may be expensive!).
 
             .. math::
-                d_\\text{pred} = P(u(m), m)
+                d_\\text{pred} = P(f(m), m)
 
             Where P is a projection of the fields onto the data space.
         """
-        if u is None: u = self.prob.fields(m)
+        if f is None: f = self.prob.fields(m)
-        return Utils.mkvc(self.eval(u, m))
+        return Utils.mkvc(self.eval(f, m))
 
     @Utils.requires('prob')
     def eval(self, U, m):
@@ -233,16 +233,16 @@ class RichardsProblem(Problem.BaseTimeProblem):
         return r, J
 
     @Utils.timeIt
-    def Jfull(self, m, u=None):
+    def Jfull(self, m, f=None):
-        if u is None:
+        if f is None:
-            u = self.fields(m)
+            f = self.fields(m)
 
-        nn = len(u)-1
+        nn = len(f)-1
         Asubs, Adiags, Bs = range(nn), range(nn), range(nn)
         for ii in range(nn):
             dt = self.timeSteps[ii]
-            bc = self.getBoundaryConditions(ii, u[ii])
+            bc = self.getBoundaryConditions(ii, f[ii])
-            Asubs[ii], Adiags[ii], Bs[ii] = self.diagsJacobian(m, u[ii], u[ii+1], dt, bc)
+            Asubs[ii], Adiags[ii], Bs[ii] = self.diagsJacobian(m, f[ii], f[ii+1], dt, bc)
         Ad = sp.block_diag(Adiags)
         zRight = Utils.spzeros((len(Asubs)-1)*Asubs[0].shape[0],Adiags[0].shape[1])
         zTop = Utils.spzeros(Adiags[0].shape[0], len(Adiags)*Adiags[0].shape[1])
@@ -251,7 +251,7 @@ class RichardsProblem(Problem.BaseTimeProblem):
         B = np.array(sp.vstack(Bs).todense())
 
         Ainv = self.Solver(A, **self.solverOpts)
-        P = self.survey.evalDeriv(u, m)
+        P = self.survey.evalDeriv(f, m)
         AinvB = Ainv * B
         z = np.zeros((self.mesh.nC, B.shape[1]))
         zAinvB = np.vstack((z, AinvB))
@@ -259,41 +259,41 @@ class RichardsProblem(Problem.BaseTimeProblem):
         return J
 
     @Utils.timeIt
-    def Jvec(self, m, v, u=None):
+    def Jvec(self, m, v, f=None):
-        if u is None:
+        if f is None:
-            u = self.fields(m)
+            f = self.fields(m)
 
-        JvC = range(len(u)-1) # Cell to hold each row of the long vector.
+        JvC = range(len(f)-1) # Cell to hold each row of the long vector.
 
         # This is done via forward substitution.
-        bc = self.getBoundaryConditions(0, u[0])
+        bc = self.getBoundaryConditions(0, f[0])
-        temp, Adiag, B = self.diagsJacobian(m, u[0], u[1], self.timeSteps[0], bc)
+        temp, Adiag, B = self.diagsJacobian(m, f[0], f[1], self.timeSteps[0], bc)
         Adiaginv = self.Solver(Adiag, **self.solverOpts)
         JvC[0] = Adiaginv * (B*v)
 
-        for ii in range(1,len(u)-1):
+        for ii in range(1,len(f)-1):
-            bc = self.getBoundaryConditions(ii, u[ii])
+            bc = self.getBoundaryConditions(ii, f[ii])
-            Asub, Adiag, B = self.diagsJacobian(m, u[ii], u[ii+1], self.timeSteps[ii], bc)
+            Asub, Adiag, B = self.diagsJacobian(m, f[ii], f[ii+1], self.timeSteps[ii], bc)
             Adiaginv = self.Solver(Adiag, **self.solverOpts)
             JvC[ii] = Adiaginv * (B*v - Asub*JvC[ii-1])
 
-        P = self.survey.evalDeriv(u, m)
+        P = self.survey.evalDeriv(f, m)
         return P * np.concatenate([np.zeros(self.mesh.nC)] + JvC)
 
     @Utils.timeIt
-    def Jtvec(self, m, v, u=None):
+    def Jtvec(self, m, v, f=None):
-        if u is None:
+        if f is None:
-            u = self.field(m)
+            f = self.field(m)
 
-        P = self.survey.evalDeriv(u, m)
+        P = self.survey.evalDeriv(f, m)
         PTv = P.T*v
 
         # This is done via backward substitution.
         minus = 0
         BJtv = 0
-        for ii in range(len(u)-1,0,-1):
+        for ii in range(len(f)-1,0,-1):
-            bc = self.getBoundaryConditions(ii-1, u[ii-1])
+            bc = self.getBoundaryConditions(ii-1, f[ii-1])
-            Asub, Adiag, B = self.diagsJacobian(m, u[ii-1], u[ii], self.timeSteps[ii-1], bc)
+            Asub, Adiag, B = self.diagsJacobian(m, f[ii-1], f[ii], self.timeSteps[ii-1], bc)
             #select the correct part of v
             vpart = range((ii)*Adiag.shape[0], (ii+1)*Adiag.shape[0])
             AdiaginvT = self.Solver(Adiag.T, **self.solverOpts)

SimPEG/Problem.py

@@ -88,28 +88,28 @@ class BaseProblem(object):
         return self.survey is not None
 
     @Utils.timeIt
-    def Jvec(self, m, v, u=None):
+    def Jvec(self, m, v, f=None):
-        """Jvec(m, v, u=None)
+        """Jvec(m, v, f=None)
 
             Effect of J(m) on a vector v.
 
             :param numpy.array m: model
             :param numpy.array v: vector to multiply
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: numpy.array
             :return: Jv
         """
         raise NotImplementedError('J is not yet implemented.')
 
     @Utils.timeIt
-    def Jtvec(self, m, v, u=None):
+    def Jtvec(self, m, v, f=None):
-        """Jtvec(m, v, u=None)
+        """Jtvec(m, v, f=None)
 
             Effect of transpose of J(m) on a vector v.
 
             :param numpy.array m: model
             :param numpy.array v: vector to multiply
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: numpy.array
             :return: JTv
         """
@@ -117,28 +117,28 @@ class BaseProblem(object):
 
 
     @Utils.timeIt
-    def Jvec_approx(self, m, v, u=None):
+    def Jvec_approx(self, m, v, f=None):
-        """Jvec_approx(m, v, u=None)
+        """Jvec_approx(m, v, f=None)
 
             Approximate effect of J(m) on a vector v
 
             :param numpy.array m: model
             :param numpy.array v: vector to multiply
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: numpy.array
             :return: approxJv
         """
         return self.Jvec(m, v, u)
 
     @Utils.timeIt
-    def Jtvec_approx(self, m, v, u=None):
+    def Jtvec_approx(self, m, v, f=None):
-        """Jtvec_approx(m, v, u=None)
+        """Jtvec_approx(m, v, f=None)
 
             Approximate effect of transpose of J(m) on a vector v.
 
             :param numpy.array m: model
             :param numpy.array v: vector to multiply
-            :param numpy.array u: fields
+            :param Fields f: fields
             :rtype: numpy.array
             :return: JTv
         """
@@ -224,9 +224,9 @@ class LinearProblem(BaseProblem):
     def fields(self, m):
         return self.G.dot(m)
 
-    def Jvec(self, m, v, u=None):
+    def Jvec(self, m, v, f=None):
         return self.G.dot(v)
 
-    def Jtvec(self, m, v, u=None):
+    def Jtvec(self, m, v, f=None):
         return self.G.T.dot(v)
 

SimPEG/Survey.py

@@ -295,21 +295,21 @@ class BaseSurvey(object):
 
     @Utils.count
     @Utils.requires('prob')
-    def dpred(self, m, u=None):
+    def dpred(self, m, f=None):
-        """dpred(m, u=None)
+        """dpred(m, f=None)
 
             Create the projected data from a model.
-            The field, u, (if provided) will be used for the predicted data
+            The fields, f, (if provided) will be used for the predicted data
             instead of recalculating the fields (which may be expensive!).
 
             .. math::
 
-                d_\\text{pred} = P(u(m))
+                d_\\text{pred} = P(f(m))
 
             Where P is a projection of the fields onto the data space.
         """
-        if u is None: u = self.prob.fields(m)
+        if f is None: f = self.prob.fields(m)
-        return Utils.mkvc(self.eval(u))
+        return Utils.mkvc(self.eval(f))
 
 
     @Utils.count
@@ -337,11 +337,11 @@ class BaseSurvey(object):
         raise NotImplemented('eval is not yet implemented.')
 
     @Utils.count
-    def residual(self, m, u=None):
+    def residual(self, m, f=None):
-        """residual(m, u=None)
+        """residual(m, f=None)
 
             :param numpy.array m: geophysical model
-            :param numpy.array u: fields
+            :param numpy.array f: fields
             :rtype: numpy.array
             :return: data residual
 
@@ -352,14 +352,14 @@ class BaseSurvey(object):
                 \mu_\\text{data} = \mathbf{d}_\\text{pred} - \mathbf{d}_\\text{obs}
 
         """
-        return Utils.mkvc(self.dpred(m, u=u) - self.dobs)
+        return Utils.mkvc(self.dpred(m, f=f) - self.dobs)
 
     @property
     def isSynthetic(self):
         "Check if the data is synthetic."
         return self.mtrue is not None
 
-    def makeSyntheticData(self, m, std=0.05, u=None, force=False):
+    def makeSyntheticData(self, m, std=0.05, f=None, force=False):
         """
             Make synthetic data given a model, and a standard deviation.
 
@@ -372,7 +372,7 @@ class BaseSurvey(object):
         if getattr(self, 'dobs', None) is not None and not force:
             raise Exception('Survey already has dobs. You can use force=True to override this exception.')
         self.mtrue = m
-        self.dtrue = self.dpred(m, u=u)
+        self.dtrue = self.dpred(m, f=f)
         noise = std*abs(self.dtrue)*np.random.randn(*self.dtrue.shape)
         self.dobs = self.dtrue+noise
         self.std = self.dobs*0 + std
@@ -381,7 +381,7 @@ class BaseSurvey(object):
 class LinearSurvey(BaseSurvey):
     def eval(self, u):
         return u
-    
+
     @property
     def nD(self):
         return self.prob.G.shape[0]

tests/flow/test_Richards.py

@@ -116,8 +116,8 @@ class RichardsTests1D(unittest.TestCase):
         v = np.random.rand(self.survey.nD)
         z = np.random.rand(self.M.nC)
         Hs = self.prob.fields(self.Ks)
-        vJz = v.dot(self.prob.Jvec(self.Ks,z,u=Hs))
+        vJz = v.dot(self.prob.Jvec(self.Ks,z,f=Hs))
-        zJv = z.dot(self.prob.Jtvec(self.Ks,v,u=Hs))
+        zJv = z.dot(self.prob.Jtvec(self.Ks,v,f=Hs))
         tol = TOL*(10**int(np.log10(np.abs(zJv))))
         passed = np.abs(vJz - zJv) < tol
         print 'Richards Adjoint Test - PressureHead'
@@ -188,8 +188,8 @@ class RichardsTests2D(unittest.TestCase):
         v = np.random.rand(self.survey.nD)
         z = np.random.rand(self.M.nC)
         Hs = self.prob.fields(self.Ks)
-        vJz = v.dot(self.prob.Jvec(self.Ks,z,u=Hs))
+        vJz = v.dot(self.prob.Jvec(self.Ks,z,f=Hs))
-        zJv = z.dot(self.prob.Jtvec(self.Ks,v,u=Hs))
+        zJv = z.dot(self.prob.Jtvec(self.Ks,v,f=Hs))
         tol = TOL*(10**int(np.log10(np.abs(zJv))))
         passed = np.abs(vJz - zJv) < tol
         print '2D: Richards Adjoint Test - PressureHead'
@@ -260,8 +260,8 @@ class RichardsTests3D(unittest.TestCase):
         v = np.random.rand(self.survey.nD)
         z = np.random.rand(self.M.nC)
         Hs = self.prob.fields(self.Ks)
-        vJz = v.dot(self.prob.Jvec(self.Ks,z,u=Hs))
+        vJz = v.dot(self.prob.Jvec(self.Ks,z,f=Hs))
-        zJv = z.dot(self.prob.Jtvec(self.Ks,v,u=Hs))
+        zJv = z.dot(self.prob.Jtvec(self.Ks,v,f=Hs))
         tol = TOL*(10**int(np.log10(np.abs(zJv))))
         passed = np.abs(vJz - zJv) < tol
         print '3D: Richards Adjoint Test - PressureHead'