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- /* This file is part of Lemma, a geophysical modelling and inversion API.
- * More information is available at http://lemmasoftware.org
- */
-
- /* 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
- * @date 11/11/2016 01:47:34 PM
- * @author Trevor Irons (ti)
- * @email tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Lemma Software, LLC
- * @copyright Copyright (c) 2008, Colorado School of Mines
- */
- #ifndef LOOPINTERACTIONS
- #define LOOPINTERACTIONS
-
- #pragma once
- #include "LemmaObject.h"
- #include "LayeredEarthEM.h"
- #include "PolygonalWireAntenna.h"
- #include "EMEarth1D.h"
- #include "FieldPoints.h"
-
- #ifdef LEMMAUSEVTK6
- #include "vtkHyperOctree.h"
- #include "vtkHyperOctreeCursor.h"
- #include "vtkXMLHyperOctreeWriter.h"
- #include "vtkDoubleArray.h"
- #endif
-
- namespace Lemma {
-
- enum INTERACTION {COUPLING, INTERFERENCE, PHASE};
- /// convert enums to string saves repeated code useful for YAML serializing
- std::string enum2String(const INTERACTION& type);
-
- /**
- * \ingroup Merlin
- * \brief Class for calculating the interactions between wire loops.
- * \details The calculations are done in the frequency domain.
- */
- template< INTERACTION Type >
- class LoopInteractions : public LemmaObject {
-
- friend std::ostream &operator << (std::ostream &stream, const LoopInteractions &ob) {
- stream << ob.Serialize() << "\n---\n"; // End of doc ---
- return stream;
- }
-
- public:
-
- // ==================== LIFECYCLE =======================
-
- /**
- * Default constructor.
- * @note This method is locked, and cannot be called directly.
- * The reason that the method is public is to enable the use
- * of make_shared whilst enforcing the use of shared_ptr,
- * in c++-17, this curiosity may be resolved.
- * @see LoopInteractions::NewSP
- */
- explicit LoopInteractions ( const ctor_key& key ) : LemmaObject (key) { }
-
- /**
- * DeSerializing constructor.
- * @note This method is locked, and cannot be called directly.
- * The reason that the method is public is to enable the use
- * of make_shared whilst enforcing the use of shared_ptr,
- * in c++-17, this curiosity may be resolved.
- * @see LoopInteractions::DeSerialize
- */
- LoopInteractions ( const YAML::Node& node, const ctor_key& key) : LemmaObject(node, key) { }
-
- /**
- * Default destructor.
- * @note This method should never be called due to the mandated
- * use of smart pointers. It is necessary to keep the method
- * public in order to allow for the use of the more efficient
- * make_shared constructor.
- */
- virtual ~LoopInteractions () { }
-
- /**
- * Uses YAML to serialize this object.
- * @return a YAML::Node
- * @see LoopInteractions::DeSerialize
- */
- virtual YAML::Node Serialize() const {
- YAML::Node node = LemmaObject::Serialize();
- node.SetTag( GetName() );
-
- // Coils Transmitters & Receivers
- for ( auto txm : TxRx) {
- node[txm.first] = txm.second->Serialize();
- }
- // LayeredEarthEM
- node["SigmaModel"] = SigmaModel->Serialize();
-
- node["tol"] = tol;
- node["minLevel"] = minLevel;
- node["maxLevel"] = maxLevel;
-
- return node;
- }
-
- /*
- * Factory method for generating concrete class.
- * @return a std::shared_ptr of type LoopInteractions
- */
- static std::shared_ptr< LoopInteractions > NewSP() {
- return std::make_shared< LoopInteractions >( ctor_key() );
- }
-
- /**
- * Constructs an LoopInteractions object from a YAML::Node.
- * @see LoopInteractions::Serialize
- */
- static std::shared_ptr<LoopInteractions> DeSerialize(const YAML::Node& node) {
- if (node.Tag() != "LoopInteractions" ) {
- throw DeSerializeTypeMismatch( "LoopInteractions", node.Tag());
- }
- return std::make_shared< LoopInteractions > ( node, ctor_key() );
- } // ----- end of method LoopInteractions::DeSerialize -----
-
- // ==================== OPERATORS =======================
-
- // ==================== OPERATIONS =======================
-
- /**
- * @return std::shared_ptr<LayeredEarthEM>
- */
- inline std::shared_ptr<LayeredEarthEM> GetSigmaModel ( ) {
- return SigmaModel;
- } // ----- end of method LoopInteractions::get_SigmaModel -----
-
- /**
- * @param[in] value the 1D-EM model used for calculations
- */
- inline void SetLayeredEarthEM ( std::shared_ptr< LayeredEarthEM > value ) {
- SigmaModel = value;
- return ;
- } // ----- end of method LoopInteractions::set_SigmaModel -----
-
- /**
- *
- */
- inline void SetIntegrationSize ( const Vector3r& size ) {
- Size = size;
- return ;
- } // ----- end of method LoopInteractions::SetIntegrationSize -----
-
- /**
- *
- */
- inline void SetIntegrationOrigin ( const Vector3r& origin ) {
- Origin = origin;
- return ;
- } // ----- end of method LoopInteractions::SetIntegrationOrigin -----
-
- /**
- * Assign transmiter coils
- */
- inline void PushCoil( const std::string& label, std::shared_ptr<PolygonalWireAntenna> ant ) {
- TxRx[label] = ant;
- }
-
- /**
- * Calculates a single imaging kernel, however, phased arrays are supported
- * so that more than one transmitter and/or receiver can be specified.
- * @param[in] tx is the list of transmitters to use for a kernel, use the same labels as
- * used in PushCoil.
- * @param[in] rx is the list of receivers to use for a kernel, use the same labels as
- * used in PushCoil. @see PushCoil
- * @param[in] vtkOutput generates a VTK hyperoctree file as well, useful for visualization.
- * requires compilation of Lemma with VTK.
- */
- Complex Calculate (const std::vector< std::string >& tx, const std::vector< std::string >& rx,
- bool vtkOutput=false );
-
- /**
- * Sets the tolerance to use for making the adaptive mesh
- *
- */
- inline void SetTolerance(const Real& ttol) {
- tol = ttol;
- }
-
- inline void SetPulseDuration(const Real& taup) {
- Taup = taup;
- }
-
- // ==================== INQUIRY =======================
- /**
- * Returns the name of the underlying class, similiar to Python's type
- * @return string of class name
- */
- virtual inline std::string GetName() const {
- return CName;
- }
-
- protected:
-
- // ==================== LIFECYCLE =======================
-
- /** Copy is disabled */
- LoopInteractions( const LoopInteractions& ) = delete;
-
- private:
-
- /**
- * Returns the kernel value for an input prism
- */
- virtual Complex f( const Vector3r& r, const Real& volume , const Vector3cr& Ht, const Vector3cr& Hr);
-
- void IntegrateOnOctreeGrid( bool vtkOutput=false );
-
- /**
- * Recursive call to integrate a function on an adaptive Octree Grid.
- * For efficiency's sake the octree grid is not stored, as only the
- * integral (sum) is of interest. The logic for grid refinement is based
- * on an Octree representation of the domain. If an Octree representation
- * of the kernel is desired, call alternative version @see EvaluateKids2
- * @param[in] size gives the domain size, in metres
- * @param[in] level gives the current level of the octree grid, call with 0 initially
- * @param[in] cpos is the centre position of the parent cuboid
- */
- void EvaluateKids( const Vector3r& size, const int& level, const Vector3r& cpos,
- const Complex& parentVal );
-
- #ifdef LEMMAUSEVTK6
- /**
- * Same functionality as @see EvaluateKids, but includes generation of a VTK
- * HyperOctree, which is useful for visualization.
- */
- void EvaluateKids2( const Vector3r& size, const int& level, const Vector3r& cpos,
- const Complex& parentVal, vtkHyperOctree* octree, vtkHyperOctreeCursor* curse );
-
- void GetPosition( vtkHyperOctreeCursor* Cursor, Real* p );
- #endif
-
- // ==================== DATA MEMBERS =========================
-
- int ilay;
- int nleaves;
- int minLevel=4;
- int maxLevel=8;
-
- Real VOLSUM;
- Real tol=1e-11;
- Real Taup = .020; // Sec
-
- Complex SUM;
-
- Vector3r Size;
- Vector3r Origin;
-
- std::shared_ptr< LayeredEarthEM > SigmaModel = nullptr;
- std::shared_ptr< FieldPoints > cpoints;
-
- std::map< std::string , std::shared_ptr< PolygonalWireAntenna > > TxRx;
- std::map< std::string , std::shared_ptr< EMEarth1D > > EMEarths;
-
- #ifdef LEMMAUSEVTK
- std::map< int, Complex > LeafDict;
- std::map< int, int > LeafDictIdx;
- std::map< int, Real > LeafDictErr;
- #endif
-
- /** ASCII string representation of the class name */
- static constexpr auto CName = "LoopInteractions";
-
- }; // ----- end of class LoopInteractions -----
-
- ///////////////////////////////////////////////////////////////
- // Implimentation of non specialized args -- templated class //
- ///////////////////////////////////////////////////////////////
-
- // forward declare specs
-
- template <>
- Complex LoopInteractions<COUPLING>::f( const Vector3r& r, const Real& volume, const Vector3cr& Ht, const Vector3cr& Hr );
-
- template <>
- Complex LoopInteractions<INTERFERENCE>::f( const Vector3r& r, const Real& volume, const Vector3cr& Ht, const Vector3cr& Hr );
-
- template <>
- Complex LoopInteractions<PHASE>::f( const Vector3r& r, const Real& volume, const Vector3cr& Ht, const Vector3cr& Hr );
-
- //--------------------------------------------------------------------------------------
- // Class: LoopInteractions
- // Method: DeSerialize
- //--------------------------------------------------------------------------------------
- template< INTERACTION Type >
- Complex LoopInteractions<Type>::Calculate (const std::vector< std::string>& Tx, const std::vector<std::string >& Rx,
- bool vtkOutput ) {
-
- static bool first = false; // a little hackish
- if (!first) {
- // All EM calculations will share same field points
- cpoints = FieldPoints::NewSP();
- cpoints->SetNumberOfPoints(8);
- }
- first = true;
-
- for (auto tx : Tx) {
- // Set up EMEarth
- EMEarths[tx] = EMEarth1D::NewSP();
- EMEarths[tx]->AttachWireAntenna(TxRx[tx]);
- EMEarths[tx]->AttachLayeredEarthEM(SigmaModel);
- EMEarths[tx]->AttachFieldPoints( cpoints );
- EMEarths[tx]->SetFieldsToCalculate(H);
- // TODO query for method, altough with flat antennae, this is fastest
- EMEarths[tx]->SetHankelTransformMethod(ANDERSON801);
- EMEarths[tx]->SetTxRxMode(TX);
- TxRx[tx]->SetCurrent(1.);
- }
- for (auto rx : Rx) {
- if (EMEarths.count(rx)) {
- EMEarths[rx]->SetTxRxMode(TXRX);
- } else {
- EMEarths[rx] = EMEarth1D::NewSP();
- EMEarths[rx]->AttachWireAntenna(TxRx[rx]);
- EMEarths[rx]->AttachLayeredEarthEM(SigmaModel);
- EMEarths[rx]->AttachFieldPoints( cpoints );
- EMEarths[rx]->SetFieldsToCalculate(H);
- // TODO query for method, altough with flat antennae, this is fastest
- EMEarths[rx]->SetHankelTransformMethod(ANDERSON801);
- EMEarths[rx]->SetTxRxMode(RX);
- TxRx[rx]->SetCurrent(1.);
- }
- }
- SUM = 0;
- IntegrateOnOctreeGrid( vtkOutput );
- std::cout << "\nFinished KERNEL\n";
- EMEarths.clear();
- return SUM;
- }
-
-
- //--------------------------------------------------------------------------------------
- // Class: LoopInteractions
- // Method: IntegrateOnOctreeGrid
- //--------------------------------------------------------------------------------------
- template< INTERACTION Type >
- void LoopInteractions<Type>::IntegrateOnOctreeGrid( bool vtkOutput ) {
-
- static int count = 0;
-
- Vector3r cpos = Origin + Size/2.;
-
- VOLSUM = 0;
- nleaves = 0;
- if (!vtkOutput) {
- EvaluateKids( Size, 0, cpos, Complex(100.));
- } else {
- #ifdef LEMMAUSEVTK6
- vtkHyperOctree* oct = vtkHyperOctree::New();
- oct->SetDimension(3);
- oct->SetOrigin( Origin(0), Origin(1), Origin(2) );
- oct->SetSize( Size(0), Size(1), Size(2) );
- vtkHyperOctreeCursor* curse = oct->NewCellCursor();
- curse->ToRoot();
- EvaluateKids2( Size, 0, cpos, Complex(100.0), oct, curse );
-
- // Fill in leaf data
- vtkDoubleArray* kr = vtkDoubleArray::New();
- kr->SetNumberOfComponents(1);
- kr->SetName("Re($\\sum$)");
- kr->SetNumberOfTuples( oct->GetNumberOfLeaves() );
- vtkDoubleArray* ki = vtkDoubleArray::New();
- ki->SetNumberOfComponents(1);
- ki->SetName("Im($\\sum$)");
- ki->SetNumberOfTuples( oct->GetNumberOfLeaves() );
- vtkDoubleArray* km = vtkDoubleArray::New();
- km->SetNumberOfComponents(1);
- km->SetName("mod($\\sum$)");
- km->SetNumberOfTuples( oct->GetNumberOfLeaves() );
- vtkIntArray* kid = vtkIntArray::New();
- kid->SetNumberOfComponents(1);
- kid->SetName("ID");
- kid->SetNumberOfTuples( oct->GetNumberOfLeaves() );
- vtkIntArray* kerr = vtkIntArray::New();
- kerr->SetNumberOfComponents(1);
- kerr->SetName("nleaf");
-
- //Real LeafVol(0);
- for (auto leaf : LeafDict) {
- kr->InsertTuple1( leaf.first, std::real(leaf.second) );
- ki->InsertTuple1( leaf.first, std::imag(leaf.second) );
- km->InsertTuple1( leaf.first, std::abs(leaf.second) );
- kid->InsertTuple1( leaf.first, leaf.first );
- //LeafVol += std::real(leaf.second);
- }
- //std::cout << "\n\nLeafVol=" << LeafVol << std::endl;
-
- for (auto leaf : LeafDictIdx) {
- kerr->InsertTuple1( leaf.first, leaf.second );
- }
-
- auto kri = oct->GetLeafData()->AddArray(kr);
- auto kii = oct->GetLeafData()->AddArray(ki);
- auto kmi = oct->GetLeafData()->AddArray(km);
- auto kidi = oct->GetLeafData()->AddArray(kid);
- auto keri = oct->GetLeafData()->AddArray(kerr);
-
- auto write = vtkXMLHyperOctreeWriter::New();
- //write.SetDataModeToAscii()
- write->SetInputData(oct);
- std::string fname = std::string("octree-") + enum2String(Type) + std::string("-")
- + to_string(count) + std::string(".vto");
- write->SetFileName(fname.c_str());
- write->Write();
- write->Delete();
-
- oct->GetLeafData()->RemoveArray( kri );
- oct->GetLeafData()->RemoveArray( kii );
- oct->GetLeafData()->RemoveArray( kmi );
- oct->GetLeafData()->RemoveArray( kidi );
- oct->GetLeafData()->RemoveArray( keri );
-
- kerr->Delete();
- kid->Delete();
- kr->Delete();
- ki->Delete();
- km->Delete();
-
- curse->Delete();
- oct->Delete();
- #else
- throw std::runtime_error("IntegrateOnOctreeGrid with vtkOutput requires Lemma with VTK support");
- #endif
-
- }
- std::cout << "\nVOLSUM=" << VOLSUM << "\tActual=" << Size(0)*Size(1)*Size(2)
- << "\tDifference=" << VOLSUM - (Size(0)*Size(1)*Size(2)) << std::endl;
- count += 1;
- }
-
- //--------------------------------------------------------------------------------------
- // Class: LoopInteractions
- // Method: EvaluateKids
- //--------------------------------------------------------------------------------------
- template< INTERACTION Type >
- void LoopInteractions<Type>::EvaluateKids( const Vector3r& size, const int& level, const Vector3r& cpos,
- const Complex& parentVal ) {
-
- std::cout << "\r" << (int)(1e2*VOLSUM/(Size[0]*Size[1]*Size[2])) << "\t" << nleaves;
- std::cout.flush();
-
- // Next level step, interested in one level below
- // bitshift requires one extra, faster than, and equivalent to std::pow(2, level+1)
- Vector3r step = size.array() / (Real)(1 << (level+1) );
- Real vol = (step(0)*step(1)*step(2)); // volume of each child
-
- Vector3r pos = cpos - step/2.;
- Eigen::Matrix<Real, 8, 3> posadd = (Eigen::Matrix<Real, 8, 3>() <<
- 0, 0, 0,
- step[0], 0, 0,
- 0, step[1], 0,
- step[0], step[1], 0,
- 0, 0, step[2],
- step[0], 0, step[2],
- 0, step[1], step[2],
- step[0], step[1], step[2] ).finished();
-
- VectorXcr kvals(8); // individual kernel vals
- cpoints->ClearFields();
- for (int ichild=0; ichild<8; ++ichild) {
- Vector3r cp = pos; // Eigen complains about combining these
- cp += posadd.row(ichild);
- cpoints->SetLocation( ichild, cp );
- }
-
- Eigen::Matrix<Complex, 3, 8> Ht = Eigen::Matrix<Complex, 3, 8>::Zero();
- Eigen::Matrix<Complex, 3, 8> Hr = Eigen::Matrix<Complex, 3, 8>::Zero();
- for ( auto EMCalc : EMEarths ) {
- EMCalc.second->GetFieldPoints()->ClearFields();
- EMCalc.second->CalculateWireAntennaFields();
- switch (EMCalc.second->GetTxRxMode()) {
- case TX:
- Ht += EMCalc.second->GetFieldPoints()->GetHfield(0);
- break;
- case RX:
- Hr += EMCalc.second->GetFieldPoints()->GetHfield(0);
- break;
- case TXRX:
- Ht += EMCalc.second->GetFieldPoints()->GetHfield(0);
- Hr += EMCalc.second->GetFieldPoints()->GetHfield(0);
- break;
- default:
- break;
- }
- }
-
- for (int ichild=0; ichild<8; ++ichild) {
- Vector3r cp = pos; // Eigen complains about combining these
- cp += posadd.row(ichild);
- kvals(ichild) = f(cp, vol, Ht.col(ichild), Hr.col(ichild));
- }
-
- Complex ksum = kvals.sum(); // Kernel sum
- // Evaluate whether or not furthur splitting is needed
- if ( (std::abs(ksum-parentVal) > tol && level < maxLevel) || level < minLevel ) {
- // Not a leaf dive further in
- for (int ichild=0; ichild<8; ++ichild) {
- Vector3r cp = pos; // Eigen complains about combining these
- cp += posadd.row(ichild);
- EvaluateKids( size, level+1, cp, kvals(ichild) );
- }
- return; // not leaf
- }
- // implicit else, is a leaf
- SUM += ksum;
- VOLSUM += 8.*vol;
- nleaves += 1; // could say += 8 just as fairly
- return; // is leaf
- }
-
- #ifdef LEMMAUSEVTK6
- //--------------------------------------------------------------------------------------
- // Class: LoopInteractions
- // Method: EvaluateKids2 -- same as Evaluate Kids, but include VTK octree generation
- //--------------------------------------------------------------------------------------
- template< INTERACTION Type >
- void LoopInteractions<Type>::EvaluateKids2( const Vector3r& size, const int& level, const Vector3r& cpos,
- const Complex& parentVal, vtkHyperOctree* oct, vtkHyperOctreeCursor* curse) {
-
- std::cout << "\r" << (int)(1e2*VOLSUM/(Size[0]*Size[1]*Size[2])) << "\t" << nleaves;
- std::cout.flush();
-
- // Next level step, interested in one level below
- // bitshift requires one extra, faster than, and equivalent to std::pow(2, level+1)
- Vector3r step = size.array() / (Real)(1 << (level+1) );
- Real vol = (step(0)*step(1)*step(2)); // volume of each child
-
- Vector3r pos = cpos - step/2.;
- Eigen::Matrix<Real, 8, 3> posadd = (Eigen::Matrix<Real, 8, 3>() <<
- 0, 0, 0,
- step[0], 0, 0,
- 0, step[1], 0,
- step[0], step[1], 0,
- 0, 0, step[2],
- step[0], 0, step[2],
- 0, step[1], step[2],
- step[0], step[1], step[2] ).finished();
-
- VectorXcr kvals(8); // individual kernel vals
- cpoints->ClearFields();
- for (int ichild=0; ichild<8; ++ichild) {
- Vector3r cp = pos; // Eigen complains about combining these
- cp += posadd.row(ichild);
- cpoints->SetLocation( ichild, cp );
- }
-
- Eigen::Matrix<Complex, 3, 8> Ht = Eigen::Matrix<Complex, 3, 8>::Zero();
- Eigen::Matrix<Complex, 3, 8> Hr = Eigen::Matrix<Complex, 3, 8>::Zero();
- for ( auto EMCalc : EMEarths ) {
- //EMCalc->GetFieldPoints()->ClearFields();
- EMCalc.second->CalculateWireAntennaFields();
- switch (EMCalc.second->GetTxRxMode()) {
- case TX:
- Ht += EMCalc.second->GetFieldPoints()->GetHfield(0);
- break;
- case RX:
- Hr += EMCalc.second->GetFieldPoints()->GetHfield(0);
- break;
- case TXRX:
- Ht += EMCalc.second->GetFieldPoints()->GetHfield(0);
- Hr += EMCalc.second->GetFieldPoints()->GetHfield(0);
- break;
- default:
- break;
- }
- }
-
- for (int ichild=0; ichild<8; ++ichild) {
- Vector3r cp = pos; // Eigen complains about combining these
- cp += posadd.row(ichild);
- kvals(ichild) = f(cp, vol, Ht.col(ichild), Hr.col(ichild));
- }
-
- Complex ksum = kvals.sum(); // Kernel sum
- // Evaluate whether or not furthur splitting is needed
- if ( (std::abs(ksum-parentVal) > tol && level < maxLevel) || level < minLevel ) {
- oct->SubdivideLeaf(curse);
- for (int ichild=0; ichild<8; ++ichild) {
- curse->ToChild(ichild);
- Vector3r cp = pos; // Eigen complains about combining these
- cp += posadd.row(ichild);
- /* Test for position via alternative means */
- /*
- Real p[3];
- GetPosition(curse, p);
- if ( (Vector3r(p) - cp).norm() > 1e-8 ) {
- std::cout << "ERROR @ nleaves" << nleaves << "\n" << cp[0] << "\t" << p[0] << "\t" << cp[1] << "\t" << p[1]
- << "\t" << cp[2] << "\t" << p[2] << "\t" << vol<< std::endl;
- throw std::runtime_error("doom");
- }
- */
- /* End of position test */
- EvaluateKids2( size, level+1, cp, kvals(ichild), oct, curse );
- curse->ToParent();
- }
- return; // not a leaf
- }
- LeafDict[curse->GetLeafId()] = ksum/(8.*vol);
- LeafDictIdx[curse->GetLeafId()] = nleaves;
- SUM += ksum;
- VOLSUM += 8*vol;
- nleaves += 1;
- return; // is a leaf
- }
-
- //--------------------------------------------------------------------------------------
- // Class: LoopInteractions
- // Method: GetPosition
- //--------------------------------------------------------------------------------------
- template< INTERACTION Type >
- void LoopInteractions<Type>::GetPosition( vtkHyperOctreeCursor* Cursor, Real* p ) {
- Real ratio=1.0/(1<<(Cursor->GetCurrentLevel()));
- //step = ((Size).array() / std::pow(2.,Cursor->GetCurrentLevel()));
- p[0]=(Cursor->GetIndex(0)+.5)*ratio*this->Size[0]+this->Origin[0] ;//+ .5*step[0];
- p[1]=(Cursor->GetIndex(1)+.5)*ratio*this->Size[1]+this->Origin[1] ;//+ .5*step[1];
- p[2]=(Cursor->GetIndex(2)+.5)*ratio*this->Size[2]+this->Origin[2] ;//+ .5*step[2];
- }
- #endif
-
- } // ----- end of namespace Lemma ----
-
- /* vim: set tabstop=4 expandtab */
- /* vim: set filetype=cpp */
-
- #endif // ----- #ifndef LOOPINTERACTIONS -----
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