Updating for CWC-CSEM

CMakeLists.txt

 set(EMSCHUR3D_VERSION "\"${EMSCHUR3D_VERSION_MAJOR}.${EMSCHUR3D_VERSION_MINOR}.${EMSCHUR3D_VERSION_PATCH}\"")
 set(EMSCHUR3D_VERSION_NOQUOTES "${EMSCHUR3D_VERSION_MAJOR}.${EMSCHUR3D_VERSION_MINOR}.${EMSCHUR3D_VERSION_PATCH}")
 
-if ( LEMMA_VTK6_SUPPORT OR LEMMA_VTK7_SUPPORT ) 
+option ( LEMMA_MODULE_EMSCHUR3D TRUE )
+
+if ( LEMMA_VTK6_SUPPORT OR LEMMA_VTK7_SUPPORT OR LEMMA_VTK8_SUPPORT AND LEMMA_MODULE_EMSCHUR3D ) 
 
 	configure_file (
 		"${CMAKE_CURRENT_SOURCE_DIR}/config/EMSchur3DConfig.h.in"
 	if (	LEMMA_BUILD_EXAMPLES)
 		add_subdirectory(examples)
 	endif()
-
+else()
+	if ( LEMMA_MODULE_EMSCHUR3D )
+        message ( FATAL_ERROR
+	          "EMSChur3D requires VTK 6, 7, or 8"	
+		)
+	endif()
+       
 endif()

examples/CMakeLists.txt

 add_executable( EMSchur3D  EMSchur3D.cpp  )
+add_executable( EMSchur3D-vtk  EMSchur3D-vtk.cpp  )
 target_link_libraries(  EMSchur3D  "lemmacore" "fdem1d" "emschur3d")
+target_link_libraries(  EMSchur3D-vtk  "lemmacore" "fdem1d" "emschur3d")
 
 # Linking
 #if ( LEMMA_VTK6_SUPPORT OR LEMMA_VTK7_SUPPORT )
 
 INSTALL_TARGETS( "/share/EMSchur3D/"
     EMSchur3D
+    EMSchur3D-vtk
 )

examples/EMSchur3D-vtk.cpp

+/* 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      01/04/2018 04:34:54 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     tirons@egi.utah.edu
+ * @copyright Copyright (c) 2018, University of Utah
+ * @copyright Copyright (c) 2018, Lemma Software, LLC
+ */
+
+#include <LemmaCore>
+//#include "RectilinearGridReader.h"
+//#include "AEMSurveyReader.h"
+#include "EMSchur3D.h"
+//#include "LayeredEarthEMReader.h"
+//#include "CSymSimplicialCholesky.h"
+
+#include "vtkRectilinearGridReader.h"
+
+using namespace Lemma;
+
+int main( int argc, char** argv ) {
+
+    if (argc < 3) {
+        std::cout << "EMSchur3D  <rgrid.vtr>  <1dmod>   <source> " << std::endl;
+        std::cout << "\trgrid.vtr - VTK Rectilinear grid file containing 3D conductivity structure.\n";
+        exit( EXIT_SUCCESS );
+    }
+
+    #ifdef LEMMAUSEOMP
+    std::cout << "Eigen is using OpenMP.\n";
+    Eigen::initParallel();
+    #endif
+
+    ///////////////////////////////////////////////////
+    // Read in VTK Grid
+    auto vtr = vtkSmartPointer<vtkRectilinearGridReader>::New();
+        vtr->SetFileName( argv[1] );
+        if (!vtr->OpenVTKFile()) {
+            std::cout << "Failed to open VTK file " << argv[1] << std::endl;
+            return EXIT_FAILURE;
+        }
+        vtr->Update();
+        //std::cout << *vtr->GetOutput() << std::endl;
+    auto gimp = RectilinearGridVTKImporter::NewSP();
+        gimp->SetVTKInput( vtr->GetOutput() );
+        gimp->ConvertGrid( 0, 0, 2150 );
+
+    //////////////////////////////////////////////////
+    // Read in Layered earth, for backgound model
+    auto  layeredEarth = LayeredEarthEM::DeSerialize( YAML::LoadFile(argv[2]) );
+
+    /*
+
+    ///////////////////////////////////////////////////
+    // Read in Grid
+    auto GridRead = RectilinearGridReader::NewSP();
+        try {
+            GridRead->ReadASCIIGridFile( argv[1] );
+        } catch (std::exception& e) {
+		    std::cout << "Caught an error opening ASCII Grid file: ";
+            std::cout << e.what() << std::endl;
+		    std::cout << "enter filename or 0 to exit programme\n";
+		    std::string inp;
+		    std::cin >> inp;
+		    if (inp != "0")
+                GridRead->ReadASCIIGridFile( inp.c_str() );
+            else exit(EXIT_FAILURE);
+	    }
+
+    //////////////////////////////////////////////////
+    // Read in Layered earth, for backgound model
+    auto LayEarthRead = LayeredEarthEMReader::NewSP();
+        try {
+            LayEarthRead->ReadASCIIInputFile( argv[2] );
+        } catch (std::exception& e) {
+		    std::cout << "Caught an error opening ASCII Layered Earth file: ";
+            std::cout << e.what() << std::endl;
+		    std::cout << "enter filename or 0 to exit programme\n";
+		    std::string inp;
+		    std::cin >> inp;
+		    if (inp != "0")
+                LayEarthRead->ReadASCIIGridFile( inp.c_str() );
+            else exit(EXIT_FAILURE);
+	    }
+    */
+
+    //////////////////////////////////////////////////
+    // Read in source specification
+    auto AEMRead = AEMSurveyReader::NewSP();
+        try{
+            AEMRead->ReadASCIIAEMFile(argv[4]);
+        } catch (std::exception& e) {
+		    std::cout << "Caught an error opening ASCII AEM file: ";
+            std::cout << e.what() << std::endl;
+		    std::cout << "enter filename or 0 to exit programme\n";
+		    std::string inp;
+		    std::cin >> inp;
+		    if (inp != "0")
+                AEMRead->ReadASCIIAEMFile( inp.c_str() );
+            else exit(EXIT_FAILURE);
+	    }
+
+    //////////////////////////////////////////////////
+    // And solve
+    // Use BiCGSTAB Diagonal preconditioner
+    //auto EM3D = EMSchur3D< Eigen::BiCGSTAB<Eigen::SparseMatrix<Complex, Eigen::RowMajor>, Eigen::IncompleteLUT<Complex> > >::NewSP();
+    //auto EM3D = EMSchur3D< Eigen::BiCGSTAB<Eigen::SparseMatrix<Complex, Eigen::RowMajor> > >::NewSP();
+    auto EM3D = EMSchur3D< Eigen::LeastSquaresConjugateGradient<Eigen::SparseMatrix<Complex, Eigen::RowMajor> > >::NewSP();
+
+
+    EM3D->SetRectilinearGrid( gimp->GetGrid() );
+
+    EM3D->SetLayeredEarthEM( layeredEarth );
+    EM3D->SetAEMSurvey( AEMRead->GetSurvey() );
+    EM3D->LoadMeshToolsConductivityModel( argv[3] );
+    EM3D->SetResFileName(argv[5]);
+
+    //EM3D->SetCSolver( Lemma::SPARSELU ); // Lemma::BiCGSTAB );
+    EM3D->Solve();
+
+    exit(EXIT_SUCCESS);
+}
+

examples/EMSchur3D.cpp

     auto EM3D = EMSchur3D< Eigen::BiCGSTAB<Eigen::SparseMatrix<Complex, Eigen::RowMajor>, Eigen::IncompleteLUT<Complex> > >::NewSP();
 
     if (argc < 3) {
-        std::cout << "EMSchur3D  <rgrid>  <1dmod>  <aemsurvey> " << std::endl;
+        std::cout << "EMSchur3D  <rgrid>  <1dmod> <3dmod>  <aemsurvey> " << std::endl;
         exit( EXIT_SUCCESS );
     }
 

include/EMSchur3D.h

         logfile += to_string(isource) + std::string(".log");
         ofstream logio(logfile.c_str());
 
-        std::cout << "just logging" << std::endl;
+        std::cout << "just logging, TODO fix source" << std::endl;
 //        logio << *Source << std::endl;
         logio << *Grid << std::endl;
         logio << *LayModel << std::endl;
 
         /////////////////////////////////////////
         // Solve for RHS
+        CSolver[iw].setMaxIterations(10000);
         VectorXcr A = CSolver[iw].solve(Se);
 
 //         // Solve Real system instead
                 // << " in " << iter_done << " iterations"
               //<<  " with error " << errorn << "\t"
               << "\tInital solution error "<<   Error.norm()  // Iteritive info
-              << "\ttime " << timer.end() << std::endl;
+              << "\ttime " << timer.end() / 60. << " [m]" << std::endl;
 
         //VectorXcr ADivMAC = ADiv.array() * MAC.array().cast<Complex>();
         //logio << "|| Div(A) || on MAC grid " << ADivMAC.norm() << std::endl;
         //Phi.array() *= MAC.array().cast<Complex>(); // remove phi from air regions
 
         /* Restart if necessary */
+/*
         int nrestart(1);
         // TODO send MAC to implicitbicgstab?
         while (success == 2 && nrestart < 18 && iter_done > 1) {
             //Phi.array() *= MAC.array().cast<Complex>(); // remove phi from air regions
             nrestart += 1;
         }
+*/
 
         logio << "Implicit BiCGStab solution in " << iter_done << " iterations."
                 << " with error " << std::setprecision(8) << std::scientific << errorn << std::endl;
-        logio << "time "<< timer.end() << " [s]" << std::endl;
+        logio << "time "<< timer.end()/60. << " [m]" << std::endl;
 
 
         E = ms.array()*(D.transpose()*Phi).array(); // Temp, field due to charge
         // Report error of solutions
         Error = ((Cc.selfadjointView<Eigen::Lower>()*A).array() + E.array() - Se.array());
         logio << "\tsolution error " << Error.norm()
-              << std::fixed << std::setprecision(2) << "\ttime " << timer.end() << "\ttotal time " << timer2.end() << std::endl;
+              << std::fixed << std::setprecision(2) << "\ttime " << timer.end()/60. << "\ttotal time " << timer2.end()/60. << std::endl;
         logio.close();
 
         //////////////////////////////////////
         }
     }
 
+    template<>
+    void EMSchur3D< Eigen::LeastSquaresConjugateGradient< Eigen::SparseMatrix<Complex, Eigen::RowMajor> > > ::BuildCDirectSolver() {
+        CSolver = new Eigen::LeastSquaresConjugateGradient< Eigen::SparseMatrix<Complex, Eigen::RowMajor> > [Omegas.size()];
+        for (int iw=0; iw<Omegas.size(); ++iw) {
+            Csym = Cvec[iw].selfadjointView<Eigen::Lower>();
+            jsw_timer timer;
+            timer.begin();
+            /*  Complex system */
+            std::cout << "LeastSquaresConjugateGradient pattern analyzing C_" << iw << ",";
+            std::cout.flush();
+            CSolver[iw].analyzePattern( Csym );
+            std::cout << " done in " << timer.end() / 60. << " [m]" << std::endl;
+            // factorize
+            timer.begin();
+            std::cout << "LeastSquaresConjugateGradient factorising C_" << iw << ", ";
+            std::cout.flush();
+            CSolver[iw].factorize( Csym );
+            std::cout << " done in " << timer.end() / 60. << " [m]" << std::endl;
+        }
+    }
+
 //     template<>
 //     void EMSchur3D<   Eigen::ConjugateGradient<Eigen::SparseMatrix<Complex, Eigen::RowMajor>, Eigen::Lower > > ::BuildCDirectSolver() {
 //         CSolver = new Eigen::ConjugateGradient<Eigen::SparseMatrix<Complex, Eigen::RowMajor>, Eigen::Lower > [Omegas.size()];

include/EMSchur3DBase.h

 //                  Colorado School of Mines
 //                  US Geological Survey
 //
-//          Email:  tirons@egi.utah.edu
+//          Email:  Trevor.Irons@utah.edu
 //
 // ===========================================================================
 
     /** Sets the RectilinearGrid to use
      *  @param[in] Grid is a pointer to the Grid to be used.
      */
+    void SetRectilinearGrid( vtkRectilinearGrid* vtkGrid );
+
+    /** Sets the RectilinearGrid to use
+     *  @param[in] Grid is a pointer to the Grid to be used.
+     */
     void SetAEMSurvey( std::shared_ptr<AEMSurvey> Survey);
 
     /** Sets the prefix for results files (.log and .vtr) the source fiducial is added as well

src/EMSchur3DBase.cpp

 
     //--------------------------------------------------------------------------------------
     //       Class:  EMSchur3DBase
+    //      Method:  SetRectilinearGrid
+    //--------------------------------------------------------------------------------------
+    void EMSchur3DBase::SetRectilinearGrid ( vtkRectilinearGrid*  rGridPtr ) {
+
+        // Convert to Lemma here
+
+
+    }		// -----  end of method EMSchur3DBase::SetRectilinearGrid  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  EMSchur3DBase
     //      Method:  Setup
     //--------------------------------------------------------------------------------------
     void EMSchur3DBase::Setup (  ) {