EMEarth1D compiles, not yet tested or profiled.

Modules/FDEM1D/include/DipoleSource.h

@@ -99,7 +99,7 @@ namespace Lemma {
                     const int& irec, std::shared_ptr<LayeredEarthEM> Earth );
 
             /** Updates the receiver fields */
-            virtual void UpdateFields(const int& ifreq, std::shared_ptr<HankelTransform> Hankel, const Real& wavef);
+            virtual void UpdateFields(const int& ifreq, HankelTransform* Hankel, const Real& wavef);
 
             // ====================  ACCESS        ======================
 

Modules/FDEM1D/include/emearth1d.h → Modules/FDEM1D/include/EMEarth1D.h

@@ -8,14 +8,11 @@
   @file
   @author   Trevor Irons
   @date     12/02/2009
-  @version  $Id: emearth1d.h 266 2015-04-01 03:24:00Z tirons $
  **/
 
 #ifndef __EMEARTH1D_H
 #define __EMEARTH1D_H
 
-
-
 // forward declare these due to include cycle
 //#include "LayeredEarthEM.h"
 //#include "DipoleSource.h"
@@ -25,11 +22,11 @@
 //#include "KernelEM1DManager.h"
 
 #include "KernelEM1DSpec.h"
-#include "hankeltransformgaussianquadrature.h"
-#include "hankeltransformhankel2.h"
-#include "FHTKey.h"
-#include "FHTKey51.h"
+#include "GQChave.h"
+#include "FHTAnderson801.h"
+#include "FHTKey201.h"
 #include "FHTKey101.h"
+#include "FHTKey51.h"
 #include "QWEKey.h"
 #include "CubicSplineInterpolator.h"
 
@@ -64,7 +61,7 @@ namespace Lemma {
             // ====================  LIFECYCLE     ===========================
 
             /** Default protected constructor. */
-            EMEarth1D ( const ctor_key& );
+            explicit EMEarth1D ( const ctor_key& );
 
             /** Default protected constructor. */
 			EMEarth1D ( const YAML::Node& node, const ctor_key& );
@@ -109,7 +106,7 @@ namespace Lemma {
             // ====================  ACCESS        ===========================
 
             /** Attaches an antennae */
-            void AttachWireAntenna(WireAntenna *antennae);
+            void AttachWireAntenna( std::shared_ptr<WireAntenna> antennae);
 
             /** Attaches a dipole for calculation */
             void AttachDipoleSource( std::shared_ptr<DipoleSource> dipole);
@@ -137,19 +134,16 @@ namespace Lemma {
              *  and CalculateWireAntennaField routines.
              */
             void SolveSingleTxRxPair(const int &irec,
-                    std::shared_ptr<HankelTransform> Hankel,
+                    HankelTransform* Hankel,
                     const Real &wavef, const int &ifreq,
-                    std::shared_ptr<DipoleSource> tDipole);
+                    DipoleSource* tDipole);
 
             /** Used internally, this is the innermost loop of the MakeCalc3,
              *  and CalculateWireAntennaField routines.
              */
-            void SolveLaggedTxRxPair(const int &irec, std::shared_ptr<Hankel2> Hankel,
+            void SolveLaggedTxRxPair(const int &irec, FHTAnderson801* Hankel,
                     const Real &wavef, const int &ifreq,
-                    std::shared_ptr<PolygonalWireAntenna> antenna);
-
-            /** Removes all connections */
-            void DetachAll();
+                    PolygonalWireAntenna* antenna);
 
             // ====================  DATA MEMBERS  ===========================
 

Modules/FDEM1D/include/PolygonalWireAntenna.h

@@ -51,7 +51,11 @@ namespace Lemma {
 
             /// Makes a deep copy of this antenna with all connections except
             /// the dipole approximation.
-            std::shared_ptr<WireAntenna> Clone();
+            virtual std::shared_ptr<WireAntenna> Clone() const ;
+
+            /// Makes a deep copy of this antenna with all connections except
+            /// the dipole approximation.
+            virtual std::shared_ptr<PolygonalWireAntenna> ClonePA() const ;
 
             /**
              *  Uses YAML to serialize this object.

Modules/FDEM1D/include/QWEKey.h

@@ -12,20 +12,18 @@
  * @date      02/12/2014 10:20:18 AM
  * @version   $Id$
  * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @email     Trevor.Irons@lemmasoftware.org
  * @copyright Copyright (c) 2014, Trevor Irons
  */
 
 #ifndef  QWEKEY_INC
 #define  QWEKEY_INC
 
-#include	"hankeltransform.h"
-#include    <Eigen/Eigenvalues>
-#ifdef HAVEBOOSTSPECIALFUNCTIONS
+#include "HankelTransform.h"
+
+#include <Eigen/Eigenvalues>
 #include "boost/math/special_functions.hpp"
 #include "boost/math/special_functions/bessel.hpp"
-#endif
 
 namespace Lemma {
 
@@ -47,24 +45,37 @@ namespace Lemma {
      */
     class QWEKey : public HankelTransform {
 
-        friend std::ostream &operator<<(std::ostream &stream,
-                const QWEKey &ob);
+        friend std::ostream &operator<<(std::ostream &stream, const QWEKey &ob);
+
+        struct ctor_key {};
 
         public:
 
         // ====================  LIFECYCLE     =======================
 
+        /** Default locked constructor, use NewSP */
+        QWEKey ( const ctor_key& );
+
+        /** DeSerializing locked constructor, use DeSerialize */
+        QWEKey ( const YAML::Node& node, const ctor_key& );
+
+        /** Default destructor */
+        ~QWEKey ();
+
         /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
+         *  Factory method for generating objects.
+         *   @return std::shared_ptr< QWEKey >
+         */
+        static std::shared_ptr<QWEKey> NewSP();
+
+        /** YAML Serializing method
          */
-        static QWEKey* New();
+        YAML::Node Serialize() const;
 
         /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
+         *   Constructs an object from a YAML::Node.
          */
-        void Delete();
+        static std::shared_ptr< QWEKey > DeSerialize(const YAML::Node& node);
 
         // ====================  OPERATORS     =======================
 
@@ -72,39 +83,31 @@ namespace Lemma {
 
         // ====================  OPERATIONS    =======================
 
-
         Complex Zgauss(const int &ikk, const EMMODE &imode,
                             const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel);
+                            const Real &wavef, KernelEM1DBase* Kernel);
 
         /// Computes related kernels, if applicable, otherwise this is
         /// just a dummy function.
-        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
+        void ComputeRelated(const Real& rho, std::shared_ptr<KernelEM1DBase> Kernel);
 
-        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
+        void ComputeRelated(const Real& rho, std::vector< std::shared_ptr<KernelEM1DBase> > KernelVec);
 
-        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
+        void ComputeRelated(const Real& rho, std::shared_ptr<KernelEM1DManager> KernelManager);
 
         // ====================  ACCESS        =======================
 
         // ====================  INQUIRY       =======================
 
+        /** Returns the name of the underlying class, similiar to Python's type */
+        virtual inline std::string GetName() const {
+            return CName;
+        }
+
         protected:
 
         // ====================  LIFECYCLE     =======================
 
-        /** Default protected constructor, use New */
-        QWEKey (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~QWEKey ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
         /** Calculates Gauss quadrature weights of order N on the interval -1,1
             Algorithm from p 129 in:
             Trefethen, L. N., 2000, Spectral methods in MATLAB: Society for
@@ -185,12 +188,14 @@ namespace Lemma {
         Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic > Zans;
 
         /** Manager for related kernels to evaluate */
-        KernelEM1DManager* KernelManager;
+        std::shared_ptr<KernelEM1DManager>  KernelManager;
 
-    }; // -----  end of class  QWEKey  -----
+        /** ASCII string representation of the class name */
+        static constexpr auto CName = "QWEKey";
 
+    }; // -----  end of class  QWEKey  -----
 
-}		// -----  end of Lemma  name  -----
+} // -----  end of Lemma  name  -----
 
 #endif   // ----- #ifndef QWEKEY_INC  -----
 

Modules/FDEM1D/include/WireAntenna.h

@@ -58,7 +58,7 @@ namespace Lemma {
             /**
              * Provides deep copy
              */
-            virtual std::shared_ptr<WireAntenna> Clone();
+            virtual std::shared_ptr<WireAntenna> Clone() const ;
 
             /**
              *  Uses YAML to serialize this object.

Modules/FDEM1D/src/CMakeLists.txt

@@ -19,8 +19,9 @@ set (FDEM1DSOURCE
 	${CMAKE_CURRENT_SOURCE_DIR}/FHTKey101.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/FHTKey51.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/GQChave.cpp
-	#${CMAKE_CURRENT_SOURCE_DIR}/QWEKey.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/QWEKey.cpp
 	
+	${CMAKE_CURRENT_SOURCE_DIR}/EMEarth1D.cpp
 
 	#${CMAKE_CURRENT_SOURCE_DIR}/AEMSurvey.cpp
 	#${CMAKE_CURRENT_SOURCE_DIR}/AEMSurveyReader.cpp

Modules/FDEM1D/src/DipoleSource.cpp

@@ -739,7 +739,7 @@ namespace Lemma {
 
     }
 
-    void DipoleSource::UpdateFields( const int& ifreq, std::shared_ptr<HankelTransform> Hankel, const Real& wavef) {
+    void DipoleSource::UpdateFields( const int& ifreq, HankelTransform* Hankel, const Real& wavef) {
 
         Vector3r Pol = Phat;
 

Modules/FDEM1D/src/PolygonalWireAntenna.cpp

@@ -65,7 +65,7 @@ namespace Lemma {
         return std::make_shared<PolygonalWireAntenna>( ctor_key() );
 	}
 
-	std::shared_ptr<WireAntenna> PolygonalWireAntenna::Clone() {
+	std::shared_ptr<WireAntenna> PolygonalWireAntenna::Clone() const {
 		auto copy = PolygonalWireAntenna::NewSP();
         copy->minDipoleRatio = this->minDipoleRatio;
 		copy->minDipoleMoment = this->minDipoleMoment;
@@ -79,6 +79,21 @@ namespace Lemma {
 		return copy;
 	}
 
+    std::shared_ptr<PolygonalWireAntenna> PolygonalWireAntenna::ClonePA() const {
+		auto copy = PolygonalWireAntenna::NewSP();
+        copy->minDipoleRatio = this->minDipoleRatio;
+		copy->minDipoleMoment = this->minDipoleMoment;
+		copy->maxDipoleMoment = this->maxDipoleMoment;
+		copy->NumberOfPoints = this->NumberOfPoints;
+		copy->Freqs = this->Freqs;
+		copy->Current = this->Current;
+		copy->NumberOfTurns = this->NumberOfTurns;
+		copy->Points = this->Points;
+		//copy->Dipoles = this->Dipoles; // no, disaster
+		return copy;
+	}
+
+
     void PolygonalWireAntenna::SetMinDipoleRatio (const Real& ratio) {
         minDipoleRatio = ratio;
     }

Modules/FDEM1D/src/QWEKey.cpp

@@ -19,25 +19,19 @@
 /**
  * @file
  * @date      02/12/2014 10:28:15 AM
- * @version   $Id$
  * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @email     Trevor.Irons@lemmasoftware.org
  * @copyright Copyright (c) 2014, Trevor Irons
  */
 
 #include "QWEKey.h"
 
-//#include <Eigen/Eigenvalues>
-
 namespace Lemma {
 
     // ====================  FRIEND METHODS  =====================
 
     std::ostream &operator<<(std::ostream &stream, const QWEKey &ob) {
-
-        stream << *(HankelTransform*)(&ob);
-
+        stream << ob.Serialize()  << "\n---\n"; // End of doc ---
         return stream;
     }
 
@@ -49,22 +43,28 @@ namespace Lemma {
     // Description:  constructor (protected)
     //--------------------------------------------------------------------------------------
     //
-    QWEKey::QWEKey (const std::string& name) : HankelTransform(name), RelTol(1e-12), AbsTol(1e-32), nQuad(61), nDelay(1),
+    QWEKey::QWEKey (const ctor_key& ) : HankelTransform( ), RelTol(1e-12), AbsTol(1e-32), nQuad(61), nDelay(1),
     //QWEKey::QWEKey (const std::string& name) : HankelTransform(name), RelTol(1e-38), AbsTol(1e-48), nQuad(39), nDelay(5),
         nIntervalsMax(40) {
         BesselWeights( J0 ); // TODO experiment with zero weight (J0, J1) options, should be static one time method
     }  // -----  end of method QWEKey::QWEKey  (constructor)  -----
 
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  QWEKey
+    // Description:  constructor (locked)
+    //--------------------------------------------------------------------------------------
+    QWEKey::QWEKey( const YAML::Node& node, const ctor_key& ) : HankelTransform(node) {
+
+    }
 
     //--------------------------------------------------------------------------------------
     //       Class:  QWEKey
     //      Method:  New()
     // Description:  public constructor
     //--------------------------------------------------------------------------------------
-    QWEKey* QWEKey::New() {
-        QWEKey*  Obj = new QWEKey("QWEKey");
-        Obj->AttachTo(Obj);
-        return Obj;
+    std::shared_ptr<QWEKey> QWEKey::NewSP() {
+        return std::make_shared<QWEKey>( ctor_key() );
     }
 
     //--------------------------------------------------------------------------------------
@@ -78,20 +78,26 @@ namespace Lemma {
 
     //--------------------------------------------------------------------------------------
     //       Class:  QWEKey
-    //      Method:  Delete
-    // Description:  public destructor
+    //      Method:  DeSerialize
+    // Description:  Factory method, converts YAML node into object
     //--------------------------------------------------------------------------------------
-    void QWEKey::Delete() {
-        this->DetachFrom(this);
+    std::shared_ptr<QWEKey> QWEKey::DeSerialize( const YAML::Node& node ) {
+        if (node.Tag() != "QWEKey") {
+            throw  DeSerializeTypeMismatch( "QWEKey", node.Tag());
+        }
+        return std::make_shared<QWEKey> ( node, ctor_key() );
     }
 
     //--------------------------------------------------------------------------------------
     //       Class:  QWEKey
-    //      Method:  Release
-    // Description:  destructor (protected)
+    //      Method:  Serialize
+    // Description:  Converts object into Serialized version
     //--------------------------------------------------------------------------------------
-    void QWEKey::Release() {
-        delete this;
+    YAML::Node QWEKey::Serialize() const {
+        YAML::Node node = HankelTransform::Serialize();
+        node.SetTag( GetName() );
+        //node["LayerConductivity"] = LayerConductivity;
+        return node;
     }
 
     //--------------------------------------------------------------------------------------
@@ -100,7 +106,7 @@ namespace Lemma {
     //--------------------------------------------------------------------------------------
     Complex QWEKey::Zgauss ( const int &ikk, const EMMODE &imode,
                             const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel ) {
+                            const Real &wavef, KernelEM1DBase *Kernel ) {
         return Textrap(Kernel->GetManagerIndex(), Tn(Kernel->GetManagerIndex())) ;
     }		// -----  end of method QWEKey::Zgauss  -----
 
@@ -108,7 +114,7 @@ namespace Lemma {
     //       Class:  QWEKey
     //      Method:  ComputeRelated
     //--------------------------------------------------------------------------------------
-    void QWEKey::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
+    void QWEKey::ComputeRelated ( const Real& rho, std::shared_ptr<KernelEM1DBase> Kernel ) {
         return ;
     }		// -----  end of method QWEKey::ComputeRelated  -----
 
@@ -116,7 +122,7 @@ namespace Lemma {
     //       Class:  QWEKey
     //      Method:  ComputeRelated
     //--------------------------------------------------------------------------------------
-    void QWEKey::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
+    void QWEKey::ComputeRelated ( const Real& rho, std::vector< std::shared_ptr<KernelEM1DBase> > KernelVec ) {
         return ;
     }		// -----  end of method QWEKey::ComputeRelated  -----
 
@@ -124,7 +130,7 @@ namespace Lemma {
     //       Class:  QWEKey
     //      Method:  ComputeRelated
     //--------------------------------------------------------------------------------------
-    void QWEKey::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManagerIn ) {
+    void QWEKey::ComputeRelated ( const Real& rho, std::shared_ptr<KernelEM1DManager> KernelManagerIn ) {
         KernelManager = KernelManagerIn;  // OK becauase this is internal and we know what we are doing
 
         Lambda = Bx.array()/rho;
@@ -140,16 +146,14 @@ namespace Lemma {
     //      Method:  GaussQuadWeights
     //--------------------------------------------------------------------------------------
     void QWEKey::GaussQuadWeights(const int& N) {
-        std::cerr<<"QWEKey needs work to remove Boost, etc." << std::endl;
-        // Below works with older Eigen, need to find problem
-//         VectorXr Nv = VectorXr::LinSpaced(N-1, 1, N-1);
-//         VectorXr beta  = 0.5 / (1.-(2.*Nv.array()).pow(-2)).sqrt();
-//         MatrixXr T = MatrixXr::Zero(N,N);
-//         //std::cerr << "Eigen ERROR BELOW, QWEKey.cpp  QWEKey::GaussQuadWeights, COMMENTED OUT ";
-//         T.bottomLeftCorner(N-1, N-1) = beta.asDiagonal();
-//         Eigen::SelfAdjointEigenSolver<MatrixXr> eig( T.selfadjointView< Eigen::Lower >() ); // PROBLEM LINE
-//             GaussAbscissa = eig.eigenvalues();
-//             GaussWeights = 2.*eig.eigenvectors().row(0).array().pow(2);
+        VectorXr Nv = VectorXr::LinSpaced(N-1, 1, N-1);
+        VectorXr beta  = 0.5 / (1.-(2.*Nv.array()).pow(-2)).sqrt();
+        MatrixXr T = MatrixXr::Zero(N,N);
+        //std::cerr << "Eigen ERROR BELOW, QWEKey.cpp  QWEKey::GaussQuadWeights, COMMENTED OUT ";
+        T.bottomLeftCorner(N-1, N-1) = beta.asDiagonal();
+        Eigen::SelfAdjointEigenSolver<MatrixXr> eig( T.selfadjointView< Eigen::Lower >() );
+            GaussAbscissa = eig.eigenvalues();
+            GaussWeights = 2.*eig.eigenvectors().row(0).array().pow(2);
     }
 
     //--------------------------------------------------------------------------------------
@@ -157,7 +161,6 @@ namespace Lemma {
     //      Method:  BesselWeights
     //--------------------------------------------------------------------------------------
     void QWEKey::BesselWeights ( const sZeroType& sType ) {
-    #ifdef HAVEBOOSTSPECIALFUNCTIONS
         GaussQuadWeights(nQuad); // TODO should this be moved out of initializer?
         std::vector<Real> bz;
         xInt = VectorXr(nIntervalsMax+1);
@@ -194,9 +197,6 @@ namespace Lemma {
             if (iw == GaussWeights.size()) iw = 0;
         }
         return ;
-    # else
-        std::cerr  << "QWEKey requires Boost functionalility that is missing\n";
-    #endif
     }		// -----  end of method QWEKey::BesselWeights  -----
 
 

Modules/FDEM1D/src/WireAntenna.cpp

@@ -41,7 +41,7 @@ namespace Lemma {
         return std::make_shared<WireAntenna>( ctor_key() );
     }
 
-    std::shared_ptr<WireAntenna> WireAntenna::Clone() {
+    std::shared_ptr<WireAntenna> WireAntenna::Clone() const {
         auto copy = WireAntenna::NewSP();
 
 		copy->NumberOfPoints = this->NumberOfPoints;

Modules/FDEM1D/src/emearth1d.cpp

@@ -1,972 +0,0 @@
-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
-
-/**
-  @file
-  @author   Trevor Irons
-  @date     12/02/2009
-  @version  $Id: emearth1d.cpp 270 2015-08-24 15:45:41Z tirons $
- **/
-
-#include "emearth1d.h"
-
-#ifdef LEMMAUSEOMP
-#include "omp.h"
-#endif
-
-namespace Lemma {
-
-#ifdef HAVE_YAMLCPP
-    std::ostream &operator << (std::ostream &stream, const EMEarth1D &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-#else
-	std::ostream &operator<<(std::ostream &stream, const
-		EMEarth1D &ob) {
-
-		stream << *(LemmaObject*)(&ob);
-		stream << "Dipole source address: " << ob.Dipole << std::endl;
-		stream << "Wire antenna address: " << ob.Antenna << std::endl;
-		stream << *ob.Earth << std::endl;
-		stream << *ob.Receivers;
-		return stream;
-	}
-#endif
-
-#ifdef KIHALEE_EM1D
-    // Wrapper function for Fortran subroutine Em1D bi kihand
-    // Returns E or H fields (SLOW)
-    extern "C" { void em1dcall_(int &itype,   // source
-                            int     &ipol,    // source
-                            int     &nlay,    // Earth
-                            int     &nfreq,   // source
-                            int     &nfield,  // Calculator
-                            int     &nres,    // Receivers
-                            int     &jtype,   // N/A
-                            int     &jgamma,  // Controller
-                            double  &acc,     // Controller
-                            double  *dep,     // Earth
-                            std::complex<double> *sig,     // Earth
-                            double  *susl,    // Earth
-                            double  *sush,    // Earth
-                            double  *sustau,  // Earth
-                            double  *susalp,  // Earth
-                            double  *eprl,    // Earth
-                            double  *eprh,    // Earth
-                            double  *eprtau,  // Earth
-                            double  *epralp,  // Earth
-                            double  &finit,   // N/A
-                            double  &flimit,  // N/A
-                            double  &dlimit,  // N/A
-                            double  &lfinc,   // N/A
-                            double  &tx,      // Source
-                            double  &ty,      // Source
-                            double  &tz,      // Source
-                            double  *rxx,     // Receivers
-                            double  *rxy,     // Receivers
-                            double  *rxz,     // Receivers
-                            std::complex<double> *ex,      // Receivers
-                            std::complex<double> *ey,      //    |
-                            std::complex<double> *ez,      //    |
-                            std::complex<double> *hx,      //    |
-                            std::complex<double> *hy,      //    V
-                            std::complex<double> *hz );    //   ___
-    }
-#endif
-
-    // ====================  LIFECYCLE     ===================================
-
-    // TODO init large arrays here.
-    EMEarth1D::EMEarth1D(const std::string& name) : LemmaObject(name),
-            Dipole(nullptr), Earth(nullptr), Receivers(nullptr), Antenna(nullptr),
-            FieldsToCalculate(BOTH), HankelType(ANDERSON801), icalcinner(0), icalc(0)
-        //#ifdef HAVEBOOSTPROGRESS
-        //    , disp(0)
-        //#endif
-        {
-    }
-
-    EMEarth1D::~EMEarth1D() {
-        if (this->NumberOfReferences > 0)
-            throw DeleteObjectWithReferences( this );
-        DetachAll();
-    }
-
-    EMEarth1D* EMEarth1D::New() {
-        EMEarth1D * Obj = new EMEarth1D("EmEarth1D");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    void EMEarth1D::Delete() {
-        this->DetachFrom(this);
-    }
-
-    void EMEarth1D::Release() {
-        DetachAll();
-        delete this;
-    }
-
-    #ifdef HAVE_YAMLCPP
-    YAML::Node EMEarth1D::Serialize() const {
-        YAML::Node node = LemmaObject::Serialize();
-
-        node["FieldsToCalculate"] = enum2String(FieldsToCalculate);
-        node["HankelType"] = enum2String(HankelType);
-
-        //if (Dipole != NULL) node["Dipole"] = Dipole->Serialize();
-        if (Earth != NULL)     node["Earth"] = Earth->Serialize();
-        //if (Receivers != NULL) node["Receivers"] = Receivers->Serialize(); Can be huge?
-        if (Antenna != NULL)   node["Antenna"] = Antenna->Serialize();
-
-        node.SetTag( this->Name );
-
-        return node;
-    }
-    #endif
-
-    // ====================  ACCESS        ===================================
-    void EMEarth1D::AttachDipoleSource(DipoleSource *dipoleptr) {
-        if (this->Dipole != NULL) {
-            this->Dipole->DetachFrom(this);
-        }
-        dipoleptr->AttachTo(this);
-        this->Dipole = dipoleptr;
-    }
-
-    void EMEarth1D::AttachLayeredEarthEM(LayeredEarthEM *earthptr) {
-        if (this->Earth != NULL)
-            this->Earth->DetachFrom(this);
-        earthptr->AttachTo(this);
-        this->Earth = earthptr;
-    }
-
-    void EMEarth1D::AttachReceiverPoints(ReceiverPoints *recptr) {
-        if (this->Receivers != NULL) {
-            this->Receivers->DetachFrom(this);
-        }
-
-        recptr->AttachTo(this);
-        this->Receivers = recptr;
-
-        if (Receivers == NULL) {
-            std::cout << "NULL Receivers in emearth1d.cpp " << std::endl;
-            return;
-        }
-
-        if (Dipole != NULL) {
-            switch (FieldsToCalculate) {
-                case E:
-                    Receivers->SetNumberOfBinsE(Dipole->GetNumberOfFrequencies());
-                    break;
-                case H:
-                    Receivers->SetNumberOfBinsH(Dipole->GetNumberOfFrequencies());
-                    break;
-                case BOTH:
-                    Receivers->SetNumberOfBinsE(Dipole->GetNumberOfFrequencies());
-                    Receivers->SetNumberOfBinsH(Dipole->GetNumberOfFrequencies());
-                    break;
-            }
-        } else if (Antenna != NULL) {
-            switch (FieldsToCalculate) {
-                case E:
-                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
-                    break;
-                case H:
-                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
-                    break;
-                case BOTH:
-                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
-                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
-                    break;
-            }
-
-        }
-
-    }
-
-    void EMEarth1D::AttachWireAntenna(WireAntenna *antennae) {
-        if (this->Antenna != NULL) {
-            this->Antenna->DetachFrom(this);
-        }
-        antennae->AttachTo(this);
-        this->Antenna = antennae;
-    }
-
-    void EMEarth1D::SetFieldsToCalculate(const FIELDCALCULATIONS &calc) {
-        FieldsToCalculate = calc;
-    }
-
-    void EMEarth1D::SetHankelTransformMethod( const HANKELTRANSFORMTYPE &type) {
-        HankelType = type;
-    }
-
-    void EMEarth1D::Query() {
-        std::cout << "EmEarth1D::Query()" << std::endl;
-
-        std::cout << "Dipole " << Dipole;
-        if (Dipole) std::cout << *Dipole << std::endl;
-
-        std::cout << "Earth " << Earth;
-        if (Earth) std::cout << *Earth << std::endl;
-
-        std::cout << "Receivers " << Earth;
-        if (Earth) std::cout << *Receivers << std::endl;
-
-        std::cout << "Antenna " << Earth;
-        if (Antenna) std::cout << *Antenna << std::endl;
-
-        std::cout << "icalc " << icalc << std::endl;
-
-        std::cout << "icalcinner " << icalcinner << std::endl;
-    }
-
-    // ====================  OPERATIONS    ===================================
-    void EMEarth1D::DetachAll() {
-
-        if (this->Dipole != NULL){
-            this->Dipole->DetachFrom(this);
-        }
-        Dipole = NULL;
-
-        if (this->Receivers != NULL){
-            this->Receivers->DetachFrom(this);
-        }
-        Receivers = NULL;
-
-        if (this->Earth != NULL){
-            this->Earth->DetachFrom(this);
-        }
-        Earth = NULL;
-
-        if (this->Antenna != NULL){
-            this->Antenna->DetachFrom(this);
-        }
-        Antenna = NULL;
-    }
-
-    void EMEarth1D::CalculateWireAntennaFields(bool progressbar) {
-
-        #ifdef HAVEBOOSTPROGRESS
-        boost::progress_display *disp;
-        #endif
-
-        if (Earth == NULL) {
-            throw NullEarth();
-        }
-        if (Receivers == NULL) {
-            throw NullReceivers();
-        }
-        if (Antenna == NULL) {
-            throw NullAntenna();
-        }
-        if (Dipole != NULL) {
-            throw DipoleSourceSpecifiedForWireAntennaCalc();
-        }
-
-        Receivers->ClearFields();
-
-        // Check to make sure Receivers are set up for all calculations
-        switch(FieldsToCalculate) {
-            case E:
-                if (Receivers->NumberOfBinsE != Antenna->GetNumberOfFrequencies())
-                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
-                break;
-            case H:
-                if (Receivers->NumberOfBinsH != Antenna->GetNumberOfFrequencies())
-                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
-                break;
-            case BOTH:
-                if (Receivers->NumberOfBinsH != Antenna->GetNumberOfFrequencies())
-                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
-                if (Receivers->NumberOfBinsE != Antenna->GetNumberOfFrequencies())
-                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
-                break;
-        }
-
-        if (Antenna->GetName() == std::string("PolygonalWireAntenna") || Antenna->GetName() == std::string("TEMTransmitter") ) {
-
-            icalc += 1;
-
-            // Check to see if they are all on a plane? If so we can do this fast
-            /* TODO FIX THIS ISSUES */
-            if (Antenna->IsHorizontallyPlanar() && HankelType == ANDERSON801) {
-                //std::cout << "Lag baby lag" << std::endl;
-                for (int ifreq=0; ifreq<Antenna->GetNumberOfFrequencies();++ifreq) {
-                    //std::cout << "Num Recs" <<  Receivers->GetNumberOfReceivers() << std::endl;
-                    Real wavef = 2.*PI* Antenna->GetFrequency(ifreq);
-                    #ifdef LEMMAUSEOMP
-                    #pragma omp parallel
-                    {
-                    #endif
-                    Hankel2* Hankel = Hankel2::New();
-                    #ifdef LEMMAUSEOMP
-                    #pragma omp for schedule(static, 1)
-                    #endif
-                    for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
-                    //for (int irec=0; irec<2; ++irec) { // TODO FIXME BELO
-                        PolygonalWireAntenna *AntCopy = static_cast<PolygonalWireAntenna*>(this->Antenna)->Clone();
-                        SolveLaggedTxRxPair(irec, Hankel, wavef, ifreq, AntCopy);
-                        AntCopy->Delete();
-                        //exit(0);
-                    }
-                    //Receivers->ClearFields(); // FIXME DEBUG TODO
-                    Hankel->Delete();
-                    #ifdef LEMMAUSEOMP
-                    }
-                    #endif
-                }
-            } else
-            if (Receivers->GetNumberOfReceivers() > Antenna->GetNumberOfFrequencies()) {
-
-                //std::cout << "freq parallel #1" << std::endl;
-                //** Progress display bar for long calculations */
-                #ifdef HAVEBOOSTPROGRESS
-                if (progressbar) {
-                    disp = new boost::progress_display( Receivers->GetNumberOfReceivers()*Antenna->GetNumberOfFrequencies() );
-                }
-                #endif
-
-                // parallelise across receivers
-                #ifdef LEMMAUSEOMP
-                #pragma omp parallel
-                #endif
-                { // OpenMP Parallel Block
-                    // Since these antennas change we need a local copy for each
-                    // thread.
-                    PolygonalWireAntenna *AntCopy =
-                            static_cast<PolygonalWireAntenna*>(this->Antenna)->Clone();
-
-                    HankelTransform* Hankel;
-                    switch (HankelType) {
-                        case ANDERSON801:
-                            Hankel = Hankel2::New();
-                            break;
-                        case CHAVE:
-                            Hankel = HankelTransformGaussianQuadrature::New();
-                            break;
-                        case FHTKEY201:
-                            Hankel = FHTKey::New();
-                            break;
-                        case FHTKEY101:
-                            Hankel = FHTKey101::New();
-                            break;
-                        case FHTKEY51:
-                            Hankel = FHTKey51::New();
-                            break;
-                        case QWEKEY:
-                            Hankel = QWEKey::New();
-                            break;
-                        default:
-                            std::cerr << "Hankel transform cannot be created\n";
-                            exit(EXIT_FAILURE);
-                    }
-
-                    //for (int irec=tid; irec<Receivers->GetNumberOfReceivers(); irec+=nthreads) {
-                    #ifdef LEMMAUSEOMP
-                    #pragma omp for schedule(static, 1) //nowait
-                    #endif
-                    for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
-                        if (!Receivers->GetMask(irec)) {
-                            AntCopy->ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
-                            for (int idip=0; idip<AntCopy->GetNumberOfDipoles(); ++idip) {
-                                DipoleSource* tDipole = AntCopy->GetDipoleSource(idip);
-                                //#ifdef LEMMAUSEOMP
-                                //#pragma omp for schedule(static, 1)
-                                //#endif
-                                for (int ifreq=0; ifreq<tDipole->GetNumberOfFrequencies();
-                                        ++ifreq) {
-                                    // Propogation constant in free space
-                                    Real wavef   = tDipole->GetAngularFrequency(ifreq) *
-                                          std::sqrt(MU0*EPSILON0);
-                                    SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
-                                } // freq loop
-                            } // dipole loop
-                        } // mask
-                        //std::cout << "Normal Path\n";
-                        //std::cout << Receivers->GetHfield(0, irec) << std::endl;
-                        //if (irec == 1) exit(0);
-                        #ifdef HAVEBOOSTPROGRESS
-                        if (progressbar) ++(*disp);
-                        #endif
-                    } // receiver loop
-                    Hankel->Delete();
-                    AntCopy->Delete();
-                } // OMP_PARALLEL BLOCK
-            } else if (Antenna->GetNumberOfFrequencies() > 8) {
-                // parallel across frequencies
-                //std::cout << "freq parallel #2" << std::endl;
-                for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
-                    if (!Receivers->GetMask(irec)) {
-                        static_cast<PolygonalWireAntenna*>(Antenna)->
-                            ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
-                        #ifdef LEMMAUSEOMP
-                        #pragma omp parallel
-                        #endif
-                        { // OpenMP Parallel Block
-
-                            HankelTransform* Hankel;
-                            switch (HankelType) {
-                                case ANDERSON801:
-                                    Hankel = Hankel2::New();
-                                    break;
-                                case CHAVE:
-                                    Hankel = HankelTransformGaussianQuadrature::New();
-                                    break;
-                                case FHTKEY201:
-                                    Hankel = FHTKey::New();
-                                    break;
-                                case FHTKEY101:
-                                    Hankel = FHTKey101::New();
-                                    break;
-                                case FHTKEY51:
-                                    Hankel = FHTKey51::New();
-                                    break;
-                                case QWEKEY:
-                                    Hankel = QWEKey::New();
-                                    break;
-                                default:
-                                    std::cerr << "Hankel transform cannot be created\n";
-                                    exit(EXIT_FAILURE);
-                            }
-                            #ifdef LEMMAUSEOMP
-                            #pragma omp for schedule(static, 1)
-                            #endif
-                            for (int ifreq=0; ifreq<Antenna->GetNumberOfFrequencies(); ++ifreq) {
-                                for (int idip=0; idip<Antenna->GetNumberOfDipoles(); ++idip) {
-                                    DipoleSource* tDipole = Antenna->GetDipoleSource(idip);
-                                    // Propogation constant in free space
-                                    Real wavef   = tDipole->GetAngularFrequency(ifreq) *
-                                          std::sqrt(MU0*EPSILON0);
-                                    SolveSingleTxRxPair(irec, Hankel, wavef,
-                                                    ifreq, tDipole);
-                                } // dipole loop
-                            } // frequency loop
-                            Hankel->Delete();
-                        } // OMP_PARALLEL BLOCK
-                    } // mask loop
-                    #ifdef HAVEBOOSTPROGRESS
-                    //if (Receivers->GetNumberOfReceivers() > 100) {
-                    //    ++ disp;
-                    //}
-                    #endif
-                } // receiver loop
-                //std::cout << "End freq parallel " << std::endl;
-            } // Frequency Parallel
-              else {
-                //std::cout << "parallel across #3 " << std::endl;
-                for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
-                    if (!Receivers->GetMask(irec)) {
-
-                        static_cast<PolygonalWireAntenna*>(Antenna)->
-                            ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
-//                         std::cout << "Not Masked " << std::endl;
-//                         std::cout << "n Freqs " << Antenna->GetNumberOfFrequencies() << std::endl;
-//                         std::cout << "n Dipoles " << Antenna->GetNumberOfDipoles() << std::endl;
-//                         if ( !Antenna->GetNumberOfDipoles() ) {
-//                             std::cout << "NO DIPOLES!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
-// //                            std::cout << "rec location " << Receivers->GetLocation(irec) << std::endl;
-// //                        }
-
-                        #ifdef LEMMAUSEOMP
-                        #pragma omp parallel
-                        #endif
-                        { // OpenMP Parallel Block
-                            HankelTransform* Hankel;
-                            switch (HankelType) {
-                                case ANDERSON801:
-                                    Hankel = Hankel2::New();
-                                    break;
-                                case CHAVE:
-                                    Hankel = HankelTransformGaussianQuadrature::New();
-                                    break;
-                                case FHTKEY201:
-                                    Hankel = FHTKey::New();
-                                    break;
-                                case FHTKEY101:
-                                    Hankel = FHTKey101::New();
-                                    break;
-                                case FHTKEY51:
-                                    Hankel = FHTKey51::New();
-                                    break;
-                                case QWEKEY:
-                                    Hankel = QWEKey::New();
-                                    break;
-                                default:
-                                    std::cerr << "Hankel transform cannot be created\n";
-                                    exit(EXIT_FAILURE);
-                            }
-                            for (int ifreq=0; ifreq<Antenna->GetNumberOfFrequencies(); ++ifreq) {
-                                #ifdef LEMMAUSEOMP
-                                #pragma omp for schedule(static, 1)
-                                #endif
-                                for (int idip=0; idip<Antenna->GetNumberOfDipoles(); ++idip) {
-                                    //#pragma omp critical
-                                    //{
-                                    //cout << "idip=" << idip << "\tthread num=" << omp_get_thread_num() << '\n';
-                                    //}
-                                    DipoleSource* tDipole = Antenna->GetDipoleSource(idip);
-                                    // Propogation constant in free space
-                                    Real wavef   = tDipole->GetAngularFrequency(ifreq) *
-                                          std::sqrt(MU0*EPSILON0);
-                                    SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
-                                } // dipole loop
-                            } // frequency loop
-                            Hankel->Delete();
-                        } // OMP_PARALLEL BLOCK
-                    } // mask loop
-                    #ifdef HAVEBOOSTPROGRESS
-                    //if (Receivers->GetNumberOfReceivers() > 100) {
-                    //    ++ disp;
-                    //}
-                    #endif
-                } // receiver loop
-           } // Polygonal parallel logic
-        } else {
-             std::cerr << "Lemma with WireAntenna class is currently broken"
-                  << " fix or use PolygonalWireAntenna\n" << std::endl;
-             exit(EXIT_FAILURE);
-            // TODO, getting wrong answer, curiously worKernel->GetKs() with MakeCalc, maybe
-            // a threading issue, use SolveSingleTxRxPair maype instead of call
-            // to MakeCalc3? !!!
-            for (int idip=0; idip<Antenna->GetNumberOfDipoles(); ++idip) {
-                this->Dipole = Antenna->GetDipoleSource(idip);
-                MakeCalc3();
-                //++disp;
-            }
-            this->Dipole = NULL;
-        }
-
-        #ifdef HAVEBOOSTPROGRESS
-        if (progressbar) {
-            delete disp;
-        }
-        #endif
-    }
-
-    #ifdef KIHALEE_EM1D
-    void EMEarth1D::MakeCalc() {
-
-        int itype;       // 1 = elec, 2 = mag
-        switch (this->Dipole->GetDipoleSourceType()) {
-            case (GROUNDEDELECTRICDIPOLE) :
-                itype = 1;
-                break;
-            case (MAGNETICDIPOLE) :
-                itype = 2;
-                break;
-            case (UNGROUNDEDELECTRICDIPOLE) :
-                std::cerr << "Fortran routine cannot calculate ungrounded"
-                             "electric dipole\n";
-            default:
-                throw NonValidDipoleType();
-        }
-
-        int ipol ;
-        Vector3r Pol = this->Dipole->GetPolarisation();
-        if (std::abs(Pol[0]-1) < 1e-5) {
-            ipol = 1;
-        } else if (std::abs(Pol[1]-1) < 1e-5) {
-            ipol = 2;
-        } else if (std::abs(Pol[2]-1) < 1e-5) {
-            ipol = 3;
-        } else {
-            std::cerr << "Fortran routine cannot calculate arbitrary "
-                             "dipole polarisation, set to x, y, or z\n";
-        }
-
-        int nlay   =  Earth->GetNumberOfNonAirLayers();
-
-        if (nlay > MAXLAYERS) {
-            std::cerr << "FORTRAN CODE CAN ONLY HANDLE " << MAXLAYERS
-                      << " LAYERS\n";
-            throw  EarthModelWithMoreThanMaxLayers();
-        }
-
-        int nfreq  = 1;     // number of freqs
-
-        int nfield;     // field output 1 = elec, 2 = mag, 3 = both
-        switch (FieldsToCalculate) {
-            case E:
-                nfield = 1;
-                break;
-            case H:
-                nfield = 2;
-                break;
-            case BOTH:
-                nfield = 3;
-                break;
-            default:
-                throw 7;
-        }
-
-        int nres   = Receivers->GetNumberOfReceivers();
-        int jtype  = 3;     // form ouf output,
-                            // 1 = horizontal,
-                            // 2 = down hole,
-                            // 3 = freq sounding
-                            // 4 = down hole logging
-
-        int jgamma = 0;     // Units 0 = MKS (H->A/m and E->V/m)
-                            //       1 = h->Gammas   E->V/m
-
-        double acc = 0.;    // Tolerance
-
-        // TODO, fix FORTRAN calls so these arrays can be nlay long, not
-        // MAXLAYERS.
-
-        // Model Parameters
-        double *dep    = new double[MAXLAYERS];
-        dep[0] = 0.;          // We always say air starts at 0
-        for (int ilay=1; ilay<Earth->GetNumberOfLayers(); ++ilay) {
-            dep[ilay] = dep[ilay-1] + Earth->GetLayerThickness(ilay);
-            //std::cout << "Depth " << dep[ilay] << std::endl;
-        }
-
-        std::complex<double> *sig = new std::complex<double> [MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            sig[ilay-1] = (std::complex<double>)(Earth->GetLayerConductivity(ilay));
-        }
-
-        // TODO, pass these into Fortran call, and return Cole-Cole model
-        // parameters. Right now this does nothing
-        //std::complex<double> *sus   = new std::complex<double>[MAXLAYERS];
-        //std::complex<double> *epr   = new std::complex<double>[MAXLAYERS];
-
-        // Cole-Cole model stuff
-        double *susl   = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            susl[ilay-1] = Earth->GetLayerLowFreqSusceptibility(ilay);
-        }
-
-        double *sush   = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            sush[ilay-1] = Earth->GetLayerHighFreqSusceptibility(ilay);
-        }
-
-        double *sustau = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            sustau[ilay-1] = Earth->GetLayerTauSusceptibility(ilay);
-        }
-
-        double *susalp = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            susalp[ilay-1] = Earth->GetLayerBreathSusceptibility(ilay);
-        }
-
-        double *eprl   = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            eprl[ilay-1] = Earth->GetLayerLowFreqPermitivity(ilay);
-        }
-
-        double *eprh   = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            eprh[ilay-1] = Earth->GetLayerHighFreqPermitivity(ilay);
-        }
-
-        double *eprtau = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            eprtau[ilay-1] = Earth->GetLayerTauPermitivity(ilay);
-        }
-
-        double *epralp = new double[MAXLAYERS];
-        for (int ilay=1; ilay<=nlay; ++ilay) {
-            epralp[ilay-1] = Earth->GetLayerBreathPermitivity(ilay);
-        }
-
-        // Freq stuff
-        double finit  = Dipole->GetFrequency(0); //(1000);   // Starting freq
-        double flimit = Dipole->GetFrequency(0); //(1000);   // max freq
-        double dlimit = Dipole->GetFrequency(0); //(1000);   // difusion limit
-        double lfinc(1);       // no. freq per decade
-
-        // tx location jtype != 4
-        double txx = Dipole->GetLocation(0); // (0.);
-        double txy = Dipole->GetLocation(1); // (0.);
-        double txz = Dipole->GetLocation(2); // (0.);
-
-        // rx position
-        // TODO, fix Fortran program to not waste this memory
-        // maybe
-        const int MAXREC = 15;
-        double *rxx = new double [MAXREC];
-        double *rxy = new double [MAXREC];
-        double *rxz = new double [MAXREC];
-
-        std::complex<double> *ex = new std::complex<double>[MAXREC];
-        std::complex<double> *ey = new std::complex<double>[MAXREC];
-        std::complex<double> *ez = new std::complex<double>[MAXREC];
-
-        std::complex<double> *hx = new std::complex<double>[MAXREC];
-        std::complex<double> *hy = new std::complex<double>[MAXREC];
-        std::complex<double> *hz = new std::complex<double>[MAXREC];
-
-        int nres2 = MAXREC;
-        int ii=0;
-
-        for (ii=0; ii<nres-MAXREC; ii+=MAXREC) {
-
-            for (int ir=0; ir<MAXREC; ++ir) {
-                //Vector3r pos = Receivers->GetLocation(ii+ir);
-                rxx[ir] = Receivers->GetLocation(ii+ir)[0];
-                rxy[ir] = Receivers->GetLocation(ii+ir)[1];
-                rxz[ir] = Receivers->GetLocation(ii+ir)[2];
-            }
-
-            em1dcall_(itype, ipol, nlay, nfreq, nfield, nres2, jtype,
-                  jgamma, acc, dep, sig, susl, sush, sustau, susalp,
-                  eprl, eprh, eprtau, epralp, finit, flimit, dlimit,
-                  lfinc, txx, txy, txz, rxx, rxy, rxz, ex, ey, ez,
-                  hx, hy, hz);
-
-            // Scale By Moment
-            for (int ir=0; ir<MAXREC; ++ir) {
-
-                ex[ir] *= Dipole->GetMoment();
-                ey[ir] *= Dipole->GetMoment();
-                ez[ir] *= Dipole->GetMoment();
-
-                hx[ir] *= Dipole->GetMoment();
-                hy[ir] *= Dipole->GetMoment();
-                hz[ir] *= Dipole->GetMoment();
-
-                // Append values instead of setting them
-                this->Receivers->AppendEfield(0, ii+ir, (Complex)(ex[ir]),
-                                                        (Complex)(ey[ir]),
-                                                        (Complex)(ez[ir]) );
-                this->Receivers->AppendHfield(0, ii+ir, (Complex)(hx[ir]),
-                                                        (Complex)(hy[ir]),
-                                                        (Complex)(hz[ir]) );
-            }
-        }
-
-        //ii += MAXREC;
-        nres2 = 0;
-        // Perform last positions
-        for (int ir=0; ir<nres-ii; ++ir) {
-            rxx[ir] = Receivers->GetLocation(ii+ir)[0];
-            rxy[ir] = Receivers->GetLocation(ii+ir)[1];
-            rxz[ir] = Receivers->GetLocation(ii+ir)[2];
-            ++nres2;
-        }
-
-        em1dcall_(itype, ipol, nlay, nfreq, nfield, nres2, jtype,
-              jgamma, acc, dep, sig, susl, sush, sustau, susalp,
-              eprl, eprh, eprtau, epralp, finit, flimit, dlimit,
-              lfinc, txx, txy, txz, rxx, rxy, rxz, ex, ey, ez,
-              hx, hy, hz);
-
-        // Scale By Moment
-        for (int ir=0; ir<nres-ii; ++ir) {
-
-            ex[ir] *= Dipole->GetMoment();
-            ey[ir] *= Dipole->GetMoment();
-            ez[ir] *= Dipole->GetMoment();
-
-            hx[ir] *= Dipole->GetMoment();
-            hy[ir] *= Dipole->GetMoment();
-            hz[ir] *= Dipole->GetMoment();
-
-            // Append values instead of setting them
-            this->Receivers->AppendEfield(0, ii+ir, (Complex)(ex[ir]),
-                                                    (Complex)(ey[ir]),
-                                                    (Complex)(ez[ir]) );
-            this->Receivers->AppendHfield(0, ii+ir, (Complex)(hx[ir]),
-                                                    (Complex)(hy[ir]),
-                                                    (Complex)(hz[ir]) );
-
-        }
-
-        delete [] sig;
-        delete [] dep;
-
-        //delete [] sus;
-        //delete [] epr;
-
-        delete [] susl;
-        delete [] sush;
-        delete [] susalp;
-        delete [] sustau;
-
-        delete [] eprl;
-        delete [] eprh;
-        delete [] epralp;
-        delete [] eprtau;
-
-        delete [] rxx;
-        delete [] rxy;
-        delete [] rxz;
-
-        delete [] ex;
-        delete [] ey;
-        delete [] ez;
-
-        delete [] hx;
-        delete [] hy;
-        delete [] hz;
-
-    }
-#endif
-
-
-    void EMEarth1D::SolveSingleTxRxPair (const int &irec,
-                   HankelTransform *Hankel, const Real &wavef, const int &ifreq,
-                   DipoleSource *tDipole) {
-        ++icalcinner;
-
-        Real rho = (Receivers->GetLocation(irec).head<2>() - tDipole->GetLocation().head<2>()).norm();
-
-        tDipole->SetKernels(ifreq, FieldsToCalculate, Receivers, irec, Earth);
-        Hankel->ComputeRelated( rho, tDipole->GetKernelManager() );
-        tDipole->UpdateFields( ifreq,  Hankel, wavef );
-    }
-
-    void EMEarth1D::SolveLaggedTxRxPair(const int &irec, Hankel2* Hankel,
-                    const Real &wavef, const int &ifreq, PolygonalWireAntenna* antenna) {
-
-        antenna->ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
-
-        // Determine the min and max arguments
-        Real rhomin = 1e9;
-        Real rhomax = 1e-9;
-        for (int idip=0; idip<antenna->GetNumberOfDipoles(); ++idip) {
-            DipoleSource* tDipole = antenna->GetDipoleSource(idip);
-            Real rho = (Receivers->GetLocation(irec).head<2>() - tDipole->GetLocation().head<2>()).norm();
-            rhomin = std::min(rhomin, rho);
-            rhomax = std::max(rhomax, rho);
-        }
-        //std::cout << "rhomin\t" << rhomin << "\trhomax" << rhomax << std::endl;
-
-        // Determine number of lagged convolutions to do
-        // TODO, can Hankel2 adjust the lagg spacing safely?
-        int nlag = 1; // We need an extra for some reason for stability
-        Real lrho ( 1.01* rhomax );
-        while ( lrho > rhomin ) {
-            nlag += 1;
-            lrho *= Hankel->GetABSER();
-        }
-
-        //int nlag = rhomin
-        DipoleSource* tDipole = antenna->GetDipoleSource(0);
-        tDipole->SetKernels(ifreq, FieldsToCalculate, Receivers, irec, Earth);
-
-        // Instead we should pass the antenna into this so that Hankel hass all the rho arguments...
-        Hankel->ComputeLaggedRelated( 1.01* rhomax, nlag, tDipole->GetKernelManager() );
-
-        //std::cout << Hankel->GetAnswer() << std::endl;
-        //std::cout << Hankel->GetArg() << std::endl;
-
-
-        // Sort the dipoles by rho
-
-        for (int idip=0; idip<antenna->GetNumberOfDipoles(); ++idip) {
-        //for (int idip=0; idip<1; ++idip) {
-            DipoleSource* tDipole = antenna->GetDipoleSource(idip);
-            tDipole->SetKernels(ifreq, FieldsToCalculate, Receivers, irec, Earth);
-            // Pass Hankel2 a message here so it knows which one to return in Zgauss!
-            Real rho = (Receivers->GetLocation(irec).head<2>() - tDipole->GetLocation().head<2>()).norm();
-            //std::cout << " in Lagged " <<  rho << "\t" << rhomin << "\t" << rhomax << std::endl;
-            Hankel->SetLaggedArg( rho );
-            //std::cout << "out Lagged" << std::endl;
-            tDipole->UpdateFields( ifreq,  Hankel, wavef );
-        }
-        //std::cout << "Spline\n";
-        //std::cout << Receivers->GetHfield(0, irec) << std::endl;
-    }
-
-    //////////////////////////////////////////////////////////
-    // Thread safe OO Reimplimentation of KiHand's
-    // EM1DNEW.for programme
-    void EMEarth1D::MakeCalc3() {
-
-        if ( Dipole == NULL ) throw NullDipoleSource();
-
-        if (Earth == NULL) throw NullEarth();
-
-        if (Receivers == NULL) throw NullReceivers();
-
-        #ifdef LEMMAUSEOMP
-        #pragma omp parallel
-        #endif
-        { // OpenMP Parallel Block
-
-            #ifdef LEMMAUSEOMP
-            int tid = omp_get_thread_num();
-            int nthreads = omp_get_num_threads();
-            #else
-            int tid=0;
-            int nthreads=1;
-            #endif
-
-            DipoleSource* tDipole = Dipole->Clone();
-
-            HankelTransform* Hankel;
-            switch (HankelType) {
-                case ANDERSON801:
-                    Hankel = Hankel2::New();
-                    break;
-                case CHAVE:
-                    Hankel = HankelTransformGaussianQuadrature::New();
-                    break;
-                case FHTKEY201:
-                    Hankel = FHTKey::New();
-                    break;
-                case FHTKEY101:
-                    Hankel = FHTKey101::New();
-                    break;
-                case FHTKEY51:
-                    Hankel = FHTKey51::New();
-                    break;
-                case QWEKEY:
-                    Hankel = QWEKey::New();
-                    break;
-                default:
-                    std::cerr << "Hankel transform cannot be created\n";
-                    exit(EXIT_FAILURE);
-            }
-
-            if ( tDipole->GetNumberOfFrequencies() < Receivers->GetNumberOfReceivers() ) {
-                for (int ifreq=0; ifreq<tDipole->GetNumberOfFrequencies(); ++ifreq) {
-                    // Propogation constant in free space being input to Hankel
-                    Real wavef   = tDipole->GetAngularFrequency(ifreq) * std::sqrt(MU0*EPSILON0);
-                    for (int irec=tid; irec<Receivers->GetNumberOfReceivers(); irec+=nthreads) {
-                        SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
-                    }
-                }
-            } else {
-                for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
-                    for (int ifreq=tid; ifreq<tDipole->GetNumberOfFrequencies(); ifreq+=nthreads) {
-                        // Propogation constant in free space being input to Hankel
-                        Real wavef   = tDipole->GetAngularFrequency(ifreq) * std::sqrt(MU0*EPSILON0);
-                        SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
-                    }
-                }
-            }
-
-            tDipole->Delete();
-            Hankel->Delete();
-
-        } // OpenMP Parallel Block
-    }
-
-    NullReceivers::NullReceivers() :
-        runtime_error("NULL RECEIVERS") {}
-
-    NullAntenna::NullAntenna() :
-        runtime_error("NULL ANTENNA") {}
-
-    NullInstrument::NullInstrument(LemmaObject* ptr) :
-        runtime_error("NULL INSTRUMENT") {
-        std::cout << "Thrown by instance of "
-                  << ptr->GetName() << std::endl;
-    }
-
-    DipoleSourceSpecifiedForWireAntennaCalc::
-        DipoleSourceSpecifiedForWireAntennaCalc() :
-        runtime_error("DIPOLE SOURCE SPECIFIED FOR WIRE ANTENNA CALC"){}
-
-} // end of Lemma Namespace

vim/c.vim

@@ -17,7 +17,7 @@ syn keyword nspace Lemma YAML Eigen
 
 " Lemma types
 highlight leType ctermfg=Yellow guifg=Yellow
-syn keyword leType HankelTransform FHTAnderson801 FHTKey201 FHTKey101 FHTKey51 KernelEM1D KernelEM1DSpec KernelEM1DBase KernelEM1DManager DipoleSource EarthModel LayeredEarth LayeredEarthEM TEMSurvey TEMSurveyLine TEMSurveyLineRecord TEMInductiveReceiver WireAntenna PolygonalWireAntenna TEMTransmitter TEMReceiver Instrument InstrumentTem LemmaObject FieldPoints DCIPElectrode TEMSurveyData TEMSurveyLineData TEMSurveyLineRecordData  ASCIIParser CubicSplineInterpolator RectilinearGrid GridReader RectilinearGridReader RectilinearGridVTKExporter Filter WindowFilter DEMParticle DEMGrain Data DataReader 
+syn keyword leType HankelTransform FHTAnderson801 FHTKey201 FHTKey101 FHTKey51 GQChave QWEKey KernelEM1D KernelEM1DSpec KernelEM1DBase KernelEM1DManager DipoleSource EarthModel LayeredEarth LayeredEarthEM TEMSurvey TEMSurveyLine TEMSurveyLineRecord TEMInductiveReceiver WireAntenna PolygonalWireAntenna TEMTransmitter TEMReceiver Instrument InstrumentTem LemmaObject FieldPoints DCIPElectrode TEMSurveyData TEMSurveyLineData TEMSurveyLineRecordData  ASCIIParser CubicSplineInterpolator RectilinearGrid GridReader RectilinearGridReader RectilinearGridVTKExporter Filter WindowFilter DEMParticle DEMGrain Data DataReader 
 
 " Deprecated Lemma Types
 highlight dleType ctermfg=Blue guifg=Blue