Teko_Utilities.cpp

/*
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// 
// ***********************************************************************
// 
//      Teko: A package for block and physics based preconditioning
//                  Copyright 2010 Sandia Corporation 
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// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
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*/

#include "Teko_Config.h"
#include "Teko_Utilities.hpp"

// Thyra includes
#include "Thyra_MultiVectorStdOps.hpp"
#include "Thyra_ZeroLinearOpBase.hpp"
#include "Thyra_DefaultDiagonalLinearOp.hpp"
#include "Thyra_DefaultAddedLinearOp.hpp"
#include "Thyra_EpetraExtDiagScaledMatProdTransformer.hpp"
#include "Thyra_EpetraExtDiagScalingTransformer.hpp"
#include "Thyra_EpetraExtAddTransformer.hpp"
#include "Thyra_DefaultScaledAdjointLinearOp.hpp"
#include "Thyra_DefaultMultipliedLinearOp.hpp"
#include "Thyra_DefaultZeroLinearOp.hpp"
#include "Thyra_DefaultProductMultiVector.hpp"
#include "Thyra_DefaultProductVectorSpace.hpp"
#include "Thyra_MultiVectorStdOps.hpp"
#include "Thyra_VectorStdOps.hpp"
#include "Thyra_get_Epetra_Operator.hpp"
#include "Thyra_EpetraThyraWrappers.hpp"
#include "Thyra_EpetraOperatorWrapper.hpp"
#include "Thyra_EpetraLinearOp.hpp"

// Teuchos includes
#include "Teuchos_Array.hpp"

// Epetra includes
#include "Epetra_Operator.h"
#include "Epetra_CrsGraph.h"
#include "Epetra_CrsMatrix.h"
#include "Epetra_Vector.h"
#include "Epetra_Map.h"

#include "EpetraExt_Transpose_RowMatrix.h"
#include "EpetraExt_MatrixMatrix.h"

// Anasazi includes
#include "AnasaziBasicEigenproblem.hpp"
#include "AnasaziThyraAdapter.hpp"
#include "AnasaziBlockKrylovSchurSolMgr.hpp"
#include "AnasaziBlockKrylovSchur.hpp"
#include "AnasaziStatusTestMaxIters.hpp"

// Isorropia includes
#ifdef Teko_ENABLE_Isorropia
#include "Isorropia_EpetraProber.hpp"
#endif

// Teko includes
#include "Epetra/Teko_EpetraHelpers.hpp"
#include "Epetra/Teko_EpetraOperatorWrapper.hpp"

#include <cmath>

namespace Teko {

using Teuchos::rcp;
using Teuchos::rcp_dynamic_cast;
using Teuchos::RCP;
#ifdef Teko_ENABLE_Isorropia
using Isorropia::Epetra::Prober;
#endif

const Teuchos::RCP<Teuchos::FancyOStream> getOutputStream()
{ 
   Teuchos::RCP<Teuchos::FancyOStream> os = 
         Teuchos::VerboseObjectBase::getDefaultOStream(); 
  
   //os->setShowProcRank(true);
   //os->setOutputToRootOnly(-1);
   return os;
}

// distance function...not parallel...entirely internal to this cpp file
inline double dist(int dim,double * coords,int row,int col)
{
   double value = 0.0;
   for(int i=0;i<dim;i++)
      value += std::pow(coords[dim*row+i]-coords[dim*col+i],2.0);

   // the distance between the two
   return std::sqrt(value);
}

// distance function...not parallel...entirely internal to this cpp file
inline double dist(double * x,double * y,double * z,int stride,int row,int col)
{
   double value = 0.0;
   if(x!=0) value += std::pow(x[stride*row]-x[stride*col],2.0);
   if(y!=0) value += std::pow(y[stride*row]-y[stride*col],2.0);
   if(z!=0) value += std::pow(z[stride*row]-z[stride*col],2.0);

   // the distance between the two
   return std::sqrt(value);
}

RCP<Epetra_CrsMatrix> buildGraphLaplacian(int dim,double * coords,const Epetra_CrsMatrix & stencil)
{
   // allocate a new matrix with storage for the laplacian...in case of diagonals add one extra storage
   RCP<Epetra_CrsMatrix> gl = rcp(new Epetra_CrsMatrix(Copy,stencil.RowMap(),stencil.ColMap(),
                                                       stencil.MaxNumEntries()+1),true);

   // allocate an additional value for the diagonal, if neccessary
   std::vector<double> rowData(stencil.GlobalMaxNumEntries()+1);
   std::vector<int> rowInd(stencil.GlobalMaxNumEntries()+1);

   // loop over all the rows
   for(int j=0;j<gl->NumMyRows();j++) {
      int row = gl->GRID(j);
      double diagValue = 0.0;
      int diagInd = -1;
      int rowSz = 0;

      // extract a copy of this row...put it in rowData, rowIndicies
      stencil.ExtractGlobalRowCopy(row,stencil.MaxNumEntries(),rowSz,&rowData[0],&rowInd[0]);
 
      // loop over elements of row
      for(int i=0;i<rowSz;i++) {
         int col = rowInd[i];

         // is this a 0 entry masquerading as some thing else?
         double value = rowData[i];
         if(value==0) continue;

         // for nondiagonal entries
         if(row!=col) {
            double d = dist(dim,coords,row,col);
            rowData[i] = -1.0/d;
            diagValue += rowData[i];
         }
         else 
            diagInd = i;
      }
    
      // handle diagonal entry
      if(diagInd<0) { // diagonal not in row
         rowData[rowSz] = -diagValue;
         rowInd[rowSz] = row;
         rowSz++;
      }
      else { // diagonal in row
         rowData[diagInd] = -diagValue;
         rowInd[diagInd] = row;
      }

      // insert row data into graph Laplacian matrix
      TEUCHOS_TEST_FOR_EXCEPT(gl->InsertGlobalValues(row,rowSz,&rowData[0],&rowInd[0]));
   }

   gl->FillComplete();

   return gl;
}

RCP<Epetra_CrsMatrix> buildGraphLaplacian(double * x,double * y,double * z,int stride,const Epetra_CrsMatrix & stencil)
{
   // allocate a new matrix with storage for the laplacian...in case of diagonals add one extra storage
   RCP<Epetra_CrsMatrix> gl = rcp(new Epetra_CrsMatrix(Copy,stencil.RowMap(),stencil.ColMap(),
                                                       stencil.MaxNumEntries()+1),true);

   // allocate an additional value for the diagonal, if neccessary
   std::vector<double> rowData(stencil.GlobalMaxNumEntries()+1);
   std::vector<int> rowInd(stencil.GlobalMaxNumEntries()+1);

   // loop over all the rows
   for(int j=0;j<gl->NumMyRows();j++) {
      int row = gl->GRID(j);
      double diagValue = 0.0;
      int diagInd = -1;
      int rowSz = 0;

      // extract a copy of this row...put it in rowData, rowIndicies
      stencil.ExtractGlobalRowCopy(row,stencil.MaxNumEntries(),rowSz,&rowData[0],&rowInd[0]);
 
      // loop over elements of row
      for(int i=0;i<rowSz;i++) {
         int col = rowInd[i];

         // is this a 0 entry masquerading as some thing else?
         double value = rowData[i];
         if(value==0) continue;

         // for nondiagonal entries
         if(row!=col) {
            double d = dist(x,y,z,stride,row,col);
            rowData[i] = -1.0/d;
            diagValue += rowData[i];
         }
         else 
            diagInd = i;
      }
    
      // handle diagonal entry
      if(diagInd<0) { // diagonal not in row
         rowData[rowSz] = -diagValue;
         rowInd[rowSz] = row;
         rowSz++;
      }
      else { // diagonal in row
         rowData[diagInd] = -diagValue;
         rowInd[diagInd] = row;
      }

      // insert row data into graph Laplacian matrix
      TEUCHOS_TEST_FOR_EXCEPT(gl->InsertGlobalValues(row,rowSz,&rowData[0],&rowInd[0]));
   }

   gl->FillComplete();

   return gl;
}

void applyOp(const LinearOp & A,const MultiVector & x,MultiVector & y,double alpha,double beta)
{
   // Thyra::apply(*A,Thyra::NONCONJ_ELE,*x,&*y,alpha,beta);
   Thyra::apply(*A,Thyra::NOTRANS,*x,y.ptr(),alpha,beta);
}

void update(double alpha,const MultiVector & x,double beta,MultiVector & y)
{
   Teuchos::Array<double> scale;
   Teuchos::Array<Teuchos::Ptr<const Thyra::MultiVectorBase<double> > >  vec;

   // build arrays needed for linear combo
   scale.push_back(alpha);
   vec.push_back(x.ptr());

   // compute linear combination
   Thyra::linear_combination<double>(scale,vec,beta,y.ptr());
}

BlockedLinearOp getUpperTriBlocks(const BlockedLinearOp & blo,bool callEndBlockFill)
{
   int rows = blockRowCount(blo);

   TEUCHOS_ASSERT(rows==blockColCount(blo));

   RCP<const Thyra::ProductVectorSpaceBase<double> > range = blo->productRange();
   RCP<const Thyra::ProductVectorSpaceBase<double> > domain = blo->productDomain();

   // allocate new operator
   BlockedLinearOp upper = createBlockedOp();
 
   // build new operator 
   upper->beginBlockFill(rows,rows);

   for(int i=0;i<rows;i++) {
      // put zero operators on the diagonal
      // this gurantees the vector space of
      // the new operator are fully defined
      RCP<const Thyra::LinearOpBase<double> > zed 
            = Thyra::zero<double>(range->getBlock(i),domain->getBlock(i));
      upper->setBlock(i,i,zed);

      for(int j=i+1;j<rows;j++) {
         // get block i,j
         LinearOp uij = blo->getBlock(i,j);

         // stuff it in U
         if(uij!=Teuchos::null)
            upper->setBlock(i,j,uij);
      }
   }
   if(callEndBlockFill)
      upper->endBlockFill();

   return upper;
}

BlockedLinearOp getLowerTriBlocks(const BlockedLinearOp & blo,bool callEndBlockFill)
{
   int rows = blockRowCount(blo);

   TEUCHOS_ASSERT(rows==blockColCount(blo));

   RCP<const Thyra::ProductVectorSpaceBase<double> > range = blo->productRange();
   RCP<const Thyra::ProductVectorSpaceBase<double> > domain = blo->productDomain();

   // allocate new operator
   BlockedLinearOp lower = createBlockedOp();
 
   // build new operator 
   lower->beginBlockFill(rows,rows);

   for(int i=0;i<rows;i++) {
      // put zero operators on the diagonal
      // this gurantees the vector space of
      // the new operator are fully defined
      RCP<const Thyra::LinearOpBase<double> > zed 
            = Thyra::zero<double>(range->getBlock(i),domain->getBlock(i));
      lower->setBlock(i,i,zed);

      for(int j=0;j<i;j++) {
         // get block i,j
         LinearOp uij = blo->getBlock(i,j);

         // stuff it in U
         if(uij!=Teuchos::null)
            lower->setBlock(i,j,uij);
      }
   }
   if(callEndBlockFill)
      lower->endBlockFill();

   return lower;
}

BlockedLinearOp zeroBlockedOp(const BlockedLinearOp & blo)
{
   int rows = blockRowCount(blo);

   TEUCHOS_ASSERT(rows==blockColCount(blo)); // assert that matrix is square

   RCP<const Thyra::ProductVectorSpaceBase<double> > range = blo->productRange();
   RCP<const Thyra::ProductVectorSpaceBase<double> > domain = blo->productDomain();

   // allocate new operator
   BlockedLinearOp zeroOp = createBlockedOp();
 
   // build new operator 
   zeroOp->beginBlockFill(rows,rows);

   for(int i=0;i<rows;i++) {
      // put zero operators on the diagonal
      // this gurantees the vector space of
      // the new operator are fully defined
      RCP<const Thyra::LinearOpBase<double> > zed 
            = Thyra::zero<double>(range->getBlock(i),domain->getBlock(i));
      zeroOp->setBlock(i,i,zed);
   }

   return zeroOp;
}

bool isZeroOp(const LinearOp op)
{
   // if operator is null...then its zero!
   if(op==Teuchos::null) return true;

   // try to cast it to a zero linear operator
   const LinearOp test = rcp_dynamic_cast<const Thyra::ZeroLinearOpBase<double> >(op);

   // if it works...then its zero...otherwise its null
   return test!=Teuchos::null;
}

ModifiableLinearOp getAbsRowSumMatrix(const LinearOp & op)
{
   RCP<const Epetra_CrsMatrix> eCrsOp;

   try {
      // get Epetra_Operator
      RCP<const Epetra_Operator> eOp = Thyra::get_Epetra_Operator(*op);

      // cast it to a CrsMatrix
      eCrsOp = rcp_dynamic_cast<const Epetra_CrsMatrix>(eOp,true);
   }
   catch (std::exception & e) {
      RCP<Teuchos::FancyOStream> out = Teuchos::VerboseObjectBase::getDefaultOStream();

      *out << "Teko: getAbsRowSumMatrix requires an Epetra_CrsMatrix\n";
      *out << "    Could not extract an Epetra_Operator from a \"" << op->description() << std::endl;
      *out << "           OR\n";
      *out << "    Could not cast an Epetra_Operator to a Epetra_CrsMatrix\n";
      *out << std::endl;
      *out << "*** THROWN EXCEPTION ***\n";
      *out << e.what() << std::endl;
      *out << "************************\n";
      
      throw e;
   }

   // extract diagonal
   const RCP<Epetra_Vector> ptrDiag = rcp(new Epetra_Vector(eCrsOp->RowMap()));
   Epetra_Vector & diag = *ptrDiag;
   
   // compute absolute value row sum
   diag.PutScalar(0.0);
   for(int i=0;i<eCrsOp->NumMyRows();i++) {
      double * values = 0;
      int numEntries;
      eCrsOp->ExtractMyRowView(i,numEntries,values);

      // build abs value row sum
      for(int j=0;j<numEntries;j++)
         diag[i] += std::abs(values[j]);
   }

   // build Thyra diagonal operator
   return Teko::Epetra::thyraDiagOp(ptrDiag,eCrsOp->RowMap(),"absRowSum( " + op->getObjectLabel() + " )");
}

ModifiableLinearOp getAbsRowSumInvMatrix(const LinearOp & op)
{
   RCP<const Epetra_CrsMatrix> eCrsOp;

   try {
      // get Epetra_Operator
      RCP<const Epetra_Operator> eOp = Thyra::get_Epetra_Operator(*op);

      // cast it to a CrsMatrix
      eCrsOp = rcp_dynamic_cast<const Epetra_CrsMatrix>(eOp,true);
   }
   catch (std::exception & e) {
      RCP<Teuchos::FancyOStream> out = Teuchos::VerboseObjectBase::getDefaultOStream();

      *out << "Teko: getAbsRowSumMatrix requires an Epetra_CrsMatrix\n";
      *out << "    Could not extract an Epetra_Operator from a \"" << op->description() << std::endl;
      *out << "           OR\n";
      *out << "    Could not cast an Epetra_Operator to a Epetra_CrsMatrix\n";
      *out << std::endl;
      *out << "*** THROWN EXCEPTION ***\n";
      *out << e.what() << std::endl;
      *out << "************************\n";
      
      throw e;
   }

   // extract diagonal
   const RCP<Epetra_Vector> ptrDiag = rcp(new Epetra_Vector(eCrsOp->RowMap()));
   Epetra_Vector & diag = *ptrDiag;
   
   // compute absolute value row sum
   diag.PutScalar(0.0);
   for(int i=0;i<eCrsOp->NumMyRows();i++) {
      double * values = 0;
      int numEntries;
      eCrsOp->ExtractMyRowView(i,numEntries,values);

      // build abs value row sum
      for(int j=0;j<numEntries;j++)
         diag[i] += std::abs(values[j]);
   }
   diag.Reciprocal(diag); // invert entries

   // build Thyra diagonal operator
   return Teko::Epetra::thyraDiagOp(ptrDiag,eCrsOp->RowMap(),"absRowSumInv( " + op->getObjectLabel() + " )");
}

ModifiableLinearOp getLumpedMatrix(const LinearOp & op)
{
   RCP<Thyra::VectorBase<double> > ones = Thyra::createMember(op->domain());
   RCP<Thyra::VectorBase<double> > diag = Thyra::createMember(op->range());

   // set to all ones
   Thyra::assign(ones.ptr(),1.0);

   // compute lumped diagonal
   // Thyra::apply(*op,Thyra::NONCONJ_ELE,*ones,&*diag);
   Thyra::apply(*op,Thyra::NOTRANS,*ones,diag.ptr());

   return rcp(new Thyra::DefaultDiagonalLinearOp<double>(diag));
}

ModifiableLinearOp getInvLumpedMatrix(const LinearOp & op)
{
   RCP<Thyra::VectorBase<double> > ones = Thyra::createMember(op->domain());
   RCP<Thyra::VectorBase<double> > diag = Thyra::createMember(op->range());

   // set to all ones
   Thyra::assign(ones.ptr(),1.0);

   // compute lumped diagonal
   Thyra::apply(*op,Thyra::NOTRANS,*ones,diag.ptr());
   Thyra::reciprocal(*diag,diag.ptr());

   return rcp(new Thyra::DefaultDiagonalLinearOp<double>(diag));
}

const ModifiableLinearOp getDiagonalOp(const LinearOp & op)
{
   RCP<const Epetra_CrsMatrix> eCrsOp;

   try {
      // get Epetra_Operator
      RCP<const Epetra_Operator> eOp = Thyra::get_Epetra_Operator(*op);

      // cast it to a CrsMatrix
      eCrsOp = rcp_dynamic_cast<const Epetra_CrsMatrix>(eOp,true);
   }
   catch (std::exception & e) {
      RCP<Teuchos::FancyOStream> out = Teuchos::VerboseObjectBase::getDefaultOStream();

      *out << "Teko: getDiagonalOp requires an Epetra_CrsMatrix\n";
      *out << "    Could not extract an Epetra_Operator from a \"" << op->description() << std::endl;
      *out << "           OR\n";
      *out << "    Could not cast an Epetra_Operator to a Epetra_CrsMatrix\n";
      *out << std::endl;
      *out << "*** THROWN EXCEPTION ***\n";
      *out << e.what() << std::endl;
      *out << "************************\n";
      
      throw e;
   }

   // extract diagonal
   const RCP<Epetra_Vector> diag = rcp(new Epetra_Vector(eCrsOp->RowMap()));
   TEUCHOS_TEST_FOR_EXCEPT(eCrsOp->ExtractDiagonalCopy(*diag));

   // build Thyra diagonal operator
   return Teko::Epetra::thyraDiagOp(diag,eCrsOp->RowMap(),"diag( " + op->getObjectLabel() + " )");
}

const MultiVector getDiagonal(const LinearOp & op)
{
   RCP<const Epetra_CrsMatrix> eCrsOp;

   try {
      // get Epetra_Operator
      RCP<const Epetra_Operator> eOp = Thyra::get_Epetra_Operator(*op);

      // cast it to a CrsMatrix
      eCrsOp = rcp_dynamic_cast<const Epetra_CrsMatrix>(eOp,true);
   }
   catch (std::exception & e) {
      RCP<Teuchos::FancyOStream> out = Teuchos::VerboseObjectBase::getDefaultOStream();

      *out << "Teko: getDiagonal requires an Epetra_CrsMatrix\n";
      *out << "    Could not extract an Epetra_Operator from a \"" << op->description() << std::endl;
      *out << "           OR\n";
      *out << "    Could not cast an Epetra_Operator to a Epetra_CrsMatrix\n";
      *out << std::endl;
      *out << "*** THROWN EXCEPTION ***\n";
      *out << e.what() << std::endl;
      *out << "************************\n";
      
      throw e;
   }

   // extract diagonal
   const RCP<Epetra_Vector> diag = rcp(new Epetra_Vector(eCrsOp->RowMap()));
   TEUCHOS_TEST_FOR_EXCEPT(eCrsOp->ExtractDiagonalCopy(*diag));

   return Thyra::create_Vector(diag,Thyra::create_VectorSpace(Teuchos::rcpFromRef(eCrsOp->RowMap())));
}

const MultiVector getDiagonal(const Teko::LinearOp & A,const DiagonalType & dt)
{
   LinearOp diagOp = Teko::getDiagonalOp(A,dt);

   Teuchos::RCP<const Thyra::MultiVectorBase<double> > v = 
         Teuchos::rcp_dynamic_cast<const Thyra::DiagonalLinearOpBase<double> >(diagOp)->getDiag(); 
   return Teuchos::rcp_const_cast<Thyra::MultiVectorBase<double> >(v);
}

const ModifiableLinearOp getInvDiagonalOp(const LinearOp & op)
{
   RCP<const Epetra_CrsMatrix> eCrsOp;

   try {
      // get Epetra_Operator
      RCP<const Epetra_Operator> eOp = Thyra::get_Epetra_Operator(*op);

      // cast it to a CrsMatrix
      eCrsOp = rcp_dynamic_cast<const Epetra_CrsMatrix>(eOp,true);
   }
   catch (std::exception & e) {
      RCP<Teuchos::FancyOStream> out = Teuchos::VerboseObjectBase::getDefaultOStream();

      *out << "Teko: getInvDiagonalOp requires an Epetra_CrsMatrix\n";
      *out << "    Could not extract an Epetra_Operator from a \"" << op->description() << std::endl;
      *out << "           OR\n";
      *out << "    Could not cast an Epetra_Operator to a Epetra_CrsMatrix\n";
      *out << std::endl;
      *out << "*** THROWN EXCEPTION ***\n";
      *out << e.what() << std::endl;
      *out << "************************\n";
      
      throw e;
   }

   // extract diagonal
   const RCP<Epetra_Vector> diag = rcp(new Epetra_Vector(eCrsOp->RowMap()));
   TEUCHOS_TEST_FOR_EXCEPT(eCrsOp->ExtractDiagonalCopy(*diag));
   diag->Reciprocal(*diag);

   // build Thyra diagonal operator
   return Teko::Epetra::thyraDiagOp(diag,eCrsOp->RowMap(),"inv(diag( " + op->getObjectLabel() + " ))");
}

const LinearOp explicitMultiply(const LinearOp & opl,const LinearOp & opm,const LinearOp & opr)
{
   // build implicit multiply
   const LinearOp implicitOp = Thyra::multiply(opl,opm,opr);

   // build transformer
   const RCP<Thyra::LinearOpTransformerBase<double> > prodTrans =
       Thyra::epetraExtDiagScaledMatProdTransformer();

   // build operator and multiply
   const RCP<Thyra::LinearOpBase<double> > explicitOp = prodTrans->createOutputOp();
   prodTrans->transform(*implicitOp,explicitOp.ptr());
   explicitOp->setObjectLabel("explicit( " + opl->getObjectLabel() +
                                     " * " + opm->getObjectLabel() +
                                     " * " + opr->getObjectLabel() + " )");

   return explicitOp;
}

const ModifiableLinearOp explicitMultiply(const LinearOp & opl,const LinearOp & opm,const LinearOp & opr,
                                          const ModifiableLinearOp & destOp)
{
   // build implicit multiply
   const LinearOp implicitOp = Thyra::multiply(opl,opm,opr);

   // build transformer
   const RCP<Thyra::LinearOpTransformerBase<double> > prodTrans =
       Thyra::epetraExtDiagScaledMatProdTransformer();

   // build operator destination operator
   ModifiableLinearOp explicitOp; 

   // if neccessary build a operator to put the explicit multiply into
   if(destOp==Teuchos::null)
      explicitOp = prodTrans->createOutputOp();
   else
      explicitOp = destOp;

   // perform multiplication
   prodTrans->transform(*implicitOp,explicitOp.ptr());

   // label it
   explicitOp->setObjectLabel("explicit( " + opl->getObjectLabel() +
                                     " * " + opm->getObjectLabel() +
                                     " * " + opr->getObjectLabel() + " )");

   return explicitOp;
}

const LinearOp explicitMultiply(const LinearOp & opl,const LinearOp & opr)
{
   // build implicit multiply
   const LinearOp implicitOp = Thyra::multiply(opl,opr);

   // build a scaling transformer
   RCP<Thyra::LinearOpTransformerBase<double> > prodTrans  
         = Thyra::epetraExtDiagScalingTransformer();

   // check to see if a scaling transformer works: if not use the 
   // DiagScaledMatrixProduct transformer
   if(not prodTrans->isCompatible(*implicitOp))
       prodTrans = Thyra::epetraExtDiagScaledMatProdTransformer();

   // build operator and multiply
   const RCP<Thyra::LinearOpBase<double> > explicitOp = prodTrans->createOutputOp();
   prodTrans->transform(*implicitOp,explicitOp.ptr());
   explicitOp->setObjectLabel("explicit( " + opl->getObjectLabel() +
                                     " * " + opr->getObjectLabel() + " )");

   return explicitOp;
}

const ModifiableLinearOp explicitMultiply(const LinearOp & opl,const LinearOp & opr,
                                          const ModifiableLinearOp & destOp)
{
   // build implicit multiply
   const LinearOp implicitOp = Thyra::multiply(opl,opr);

   // build a scaling transformer
   RCP<Thyra::LinearOpTransformerBase<double> > prodTrans  
         = Thyra::epetraExtDiagScalingTransformer();

   // check to see if a scaling transformer works: if not use the 
   // DiagScaledMatrixProduct transformer
   if(not prodTrans->isCompatible(*implicitOp))
       prodTrans = Thyra::epetraExtDiagScaledMatProdTransformer();

   // build operator destination operator
   ModifiableLinearOp explicitOp; 

   // if neccessary build a operator to put the explicit multiply into
   if(destOp==Teuchos::null)
      explicitOp = prodTrans->createOutputOp();
   else
      explicitOp = destOp;

   // perform multiplication
   prodTrans->transform(*implicitOp,explicitOp.ptr());

   // label it
   explicitOp->setObjectLabel("explicit( " + opl->getObjectLabel() +
                                     " * " + opr->getObjectLabel() + " )");

   return explicitOp;
}

const LinearOp explicitAdd(const LinearOp & opl,const LinearOp & opr)
{
   // build implicit multiply
   const LinearOp implicitOp = Thyra::add(opl,opr);
 
   // build transformer
   const RCP<Thyra::LinearOpTransformerBase<double> > prodTrans =
       Thyra::epetraExtAddTransformer();

   // build operator and multiply
   const RCP<Thyra::LinearOpBase<double> > explicitOp = prodTrans->createOutputOp();
   prodTrans->transform(*implicitOp,explicitOp.ptr());
   explicitOp->setObjectLabel("explicit( " + opl->getObjectLabel() +
                                     " + " + opr->getObjectLabel() + " )");

   return explicitOp;
}

const ModifiableLinearOp explicitAdd(const LinearOp & opl,const LinearOp & opr,
                                     const ModifiableLinearOp & destOp)
{
   // build implicit multiply
   const LinearOp implicitOp = Thyra::add(opl,opr);
 
   // build transformer
   const RCP<Thyra::LinearOpTransformerBase<double> > prodTrans =
       Thyra::epetraExtAddTransformer();

   // build or reuse destination operator
   RCP<Thyra::LinearOpBase<double> > explicitOp;
   if(destOp!=Teuchos::null)
      explicitOp = destOp;
   else
      explicitOp = prodTrans->createOutputOp();

   // perform multiplication
   prodTrans->transform(*implicitOp,explicitOp.ptr());
   explicitOp->setObjectLabel("explicit( " + opl->getObjectLabel() +
                                     " + " + opr->getObjectLabel() + " )");

   return explicitOp;
}

const ModifiableLinearOp explicitSum(const LinearOp & op,
                                     const ModifiableLinearOp & destOp)
{
   // convert operators to Epetra_CrsMatrix
   const RCP<const Epetra_CrsMatrix> epetraOp =
         rcp_dynamic_cast<const Epetra_CrsMatrix>(get_Epetra_Operator(*op), true);

   if(destOp==Teuchos::null) {
      Teuchos::RCP<Epetra_Operator> epetraDest = Teuchos::rcp(new Epetra_CrsMatrix(*epetraOp));

      return Thyra::nonconstEpetraLinearOp(epetraDest);
   }

   const RCP<Epetra_CrsMatrix> epetraDest =
         rcp_dynamic_cast<Epetra_CrsMatrix>(get_Epetra_Operator(*destOp), true);

   EpetraExt::MatrixMatrix::Add(*epetraOp,false,1.0,*epetraDest,1.0);

   return destOp;
}

const LinearOp explicitTranspose(const LinearOp & op)
{
   RCP<const Epetra_Operator> eOp = Thyra::get_Epetra_Operator(*op);
   TEUCHOS_TEST_FOR_EXCEPTION(eOp==Teuchos::null,std::logic_error,
                             "Teko::explicitTranspose Not an Epetra_Operator");
   RCP<const Epetra_RowMatrix> eRowMatrixOp 
         = Teuchos::rcp_dynamic_cast<const Epetra_RowMatrix>(eOp);
   TEUCHOS_TEST_FOR_EXCEPTION(eRowMatrixOp==Teuchos::null,std::logic_error,
                             "Teko::explicitTranspose Not an Epetra_RowMatrix");

   // we now have a delete transpose operator
   EpetraExt::RowMatrix_Transpose tranposeOp;
   Epetra_RowMatrix & eMat = tranposeOp(const_cast<Epetra_RowMatrix &>(*eRowMatrixOp));

   // this copy is because of a poor implementation of the EpetraExt::Transform 
   // implementation
   Teuchos::RCP<Epetra_CrsMatrix> crsMat 
         = Teuchos::rcp(new Epetra_CrsMatrix(dynamic_cast<Epetra_CrsMatrix &>(eMat)));

   return Thyra::epetraLinearOp(crsMat);
}

const LinearOp buildDiagonal(const MultiVector & src,const std::string & lbl)
{
   RCP<Thyra::VectorBase<double> > dst = Thyra::createMember(src->range()); 
   Thyra::copy(*src->col(0),dst.ptr());
   
   return Thyra::diagonal<double>(dst,lbl);
}

const LinearOp buildInvDiagonal(const MultiVector & src,const std::string & lbl)
{
   const RCP<const Thyra::VectorBase<double> > srcV = src->col(0);
   RCP<Thyra::VectorBase<double> > dst = Thyra::createMember(srcV->range()); 
   Thyra::reciprocal<double>(*srcV,dst.ptr());

   return Thyra::diagonal<double>(dst,lbl);
}

BlockedMultiVector buildBlockedMultiVector(const std::vector<MultiVector> & mvv)
{
   Teuchos::Array<MultiVector> mvA;
   Teuchos::Array<VectorSpace> vsA;

   // build arrays of multi vectors and vector spaces
   std::vector<MultiVector>::const_iterator itr;
   for(itr=mvv.begin();itr!=mvv.end();++itr) {
      mvA.push_back(*itr);
      vsA.push_back((*itr)->range());
   }

   // construct the product vector space
   const RCP<const Thyra::DefaultProductVectorSpace<double> > vs
         = Thyra::productVectorSpace<double>(vsA);

   return Thyra::defaultProductMultiVector<double>(vs,mvA);
}

Teuchos::RCP<Thyra::VectorBase<double> > indicatorVector(
                                 const std::vector<int> & indices,
                                 const VectorSpace & vs,
                                 double onValue, double offValue)

{
   using Teuchos::RCP;
 
   // create a new vector
   RCP<Thyra::VectorBase<double> > v = Thyra::createMember<double>(vs);
   Thyra::put_scalar<double>(offValue,v.ptr()); // fill it with "off" values

   // set on values
   for(std::size_t i=0;i<indices.size();i++) 
      Thyra::set_ele<double>(indices[i],onValue,v.ptr());

   return v;
}

double computeSpectralRad(const RCP<const Thyra::LinearOpBase<double> > & A, double tol,
                          bool isHermitian,int numBlocks,int restart,int verbosity)
{
   typedef Thyra::LinearOpBase<double> OP;
   typedef Thyra::MultiVectorBase<double> MV;

   int startVectors = 1;

   // construct an initial guess
   const RCP<MV> ivec = Thyra::createMember(A->domain());
   Thyra::randomize(-1.0,1.0,ivec.ptr());
   
   RCP<Anasazi::BasicEigenproblem<double,MV,OP> > eigProb
         = rcp(new Anasazi::BasicEigenproblem<double,MV,OP>(A,ivec));
   eigProb->setNEV(1);
   eigProb->setHermitian(isHermitian);

   // set the problem up
   if(not eigProb->setProblem()) {
      // big time failure!
      return Teuchos::ScalarTraits<double>::nan();
   }

   // we want largert magnitude eigenvalue
   std::string which("LM"); // largest magnitude

   // Create the parameter list for the eigensolver
   // verbosity+=Anasazi::TimingDetails;
   Teuchos::ParameterList MyPL;
   MyPL.set( "Verbosity", verbosity );
   MyPL.set( "Which", which );
   MyPL.set( "Block Size", startVectors );
   MyPL.set( "Num Blocks", numBlocks );
   MyPL.set( "Maximum Restarts", restart ); 
   MyPL.set( "Convergence Tolerance", tol );

   // build status test manager
   // RCP<Anasazi::StatusTestMaxIters<double,MV,OP> > statTest
   //       = rcp(new Anasazi::StatusTestMaxIters<double,MV,OP>(numBlocks*(restart+1)));

   // Create the Block Krylov Schur solver
   // This takes as inputs the eigenvalue problem and the solver parameters
   Anasazi::BlockKrylovSchurSolMgr<double,MV,OP> MyBlockKrylovSchur(eigProb, MyPL );
 
   // Solve the eigenvalue problem, and save the return code
   Anasazi::ReturnType solverreturn = MyBlockKrylovSchur.solve();

   if(solverreturn==Anasazi::Unconverged) {
      double real = MyBlockKrylovSchur.getRitzValues().begin()->realpart;
      double comp = MyBlockKrylovSchur.getRitzValues().begin()->imagpart;

      return -std::abs(std::sqrt(real*real+comp*comp));

      // cout << "Anasazi::BlockKrylovSchur::solve() did not converge!" << std::endl; 
      // return -std::abs(MyBlockKrylovSchur.getRitzValues().begin()->realpart);
   }
   else { // solverreturn==Anasazi::Converged
      double real = eigProb->getSolution().Evals.begin()->realpart;
      double comp = eigProb->getSolution().Evals.begin()->imagpart;

      return std::abs(std::sqrt(real*real+comp*comp));

      // cout << "Anasazi::BlockKrylovSchur::solve() converged!" << endl;
      // return std::abs(eigProb->getSolution().Evals.begin()->realpart);
   }
}

double computeSmallestMagEig(const RCP<const Thyra::LinearOpBase<double> > & A, double tol,
                             bool isHermitian,int numBlocks,int restart,int verbosity)
{
   typedef Thyra::LinearOpBase<double> OP;
   typedef Thyra::MultiVectorBase<double> MV;

   int startVectors = 1;

   // construct an initial guess
   const RCP<MV> ivec = Thyra::createMember(A->domain());
   Thyra::randomize(-1.0,1.0,ivec.ptr());
   
   RCP<Anasazi::BasicEigenproblem<double,MV,OP> > eigProb
         = rcp(new Anasazi::BasicEigenproblem<double,MV,OP>(A,ivec));
   eigProb->setNEV(1);
   eigProb->setHermitian(isHermitian);

   // set the problem up
   if(not eigProb->setProblem()) {
      // big time failure!
      return Teuchos::ScalarTraits<double>::nan();
   }

   // we want largert magnitude eigenvalue
   std::string which("SM"); // smallest magnitude

   // Create the parameter list for the eigensolver
   Teuchos::ParameterList MyPL;
   MyPL.set( "Verbosity", verbosity );
   MyPL.set( "Which", which );
   MyPL.set( "Block Size", startVectors );
   MyPL.set( "Num Blocks", numBlocks );
   MyPL.set( "Maximum Restarts", restart ); 
   MyPL.set( "Convergence Tolerance", tol );

   // build status test manager
   // RCP<Anasazi::StatusTestMaxIters<double,MV,OP> > statTest
   //       = rcp(new Anasazi::StatusTestMaxIters<double,MV,OP>(10));

   // Create the Block Krylov Schur solver
   // This takes as inputs the eigenvalue problem and the solver parameters
   Anasazi::BlockKrylovSchurSolMgr<double,MV,OP> MyBlockKrylovSchur(eigProb, MyPL );
 
   // Solve the eigenvalue problem, and save the return code
   Anasazi::ReturnType solverreturn = MyBlockKrylovSchur.solve();

   if(solverreturn==Anasazi::Unconverged) {
      // cout << "Anasazi::BlockKrylovSchur::solve() did not converge! " << std::endl;
      return -std::abs(MyBlockKrylovSchur.getRitzValues().begin()->realpart);
   }
   else { // solverreturn==Anasazi::Converged
      // cout << "Anasazi::BlockKrylovSchur::solve() converged!" << endl;
      return std::abs(eigProb->getSolution().Evals.begin()->realpart);
   }
}

ModifiableLinearOp getDiagonalOp(const Teko::LinearOp & A,const DiagonalType & dt)
{
   switch(dt) {
   case Diagonal:
      return getDiagonalOp(A);  
   case Lumped:
      return getLumpedMatrix(A);  
   case AbsRowSum:
      return getAbsRowSumMatrix(A);  
   case NotDiag:
   default:
      TEUCHOS_TEST_FOR_EXCEPT(true);
   };

   return Teuchos::null;
}

ModifiableLinearOp getInvDiagonalOp(const Teko::LinearOp & A,const Teko::DiagonalType & dt)
{
   switch(dt) {
   case Diagonal:
      return getInvDiagonalOp(A);  
   case Lumped:
      return getInvLumpedMatrix(A);  
   case AbsRowSum:
      return getAbsRowSumInvMatrix(A);  
   case NotDiag:
   default:
      TEUCHOS_TEST_FOR_EXCEPT(true);
   };

   return Teuchos::null;
}

std::string getDiagonalName(const DiagonalType & dt)
{
   switch(dt) {
   case Diagonal:
      return "Diagonal";
   case Lumped:
      return "Lumped";
   case AbsRowSum:
      return "AbsRowSum";
   case NotDiag:
      return "NotDiag";
   case BlkDiag:
      return "BlkDiag";
   };

   return "<error>";
}

DiagonalType getDiagonalType(std::string name)
{
   if(name=="Diagonal")
      return Diagonal;
   if(name=="Lumped")
     return Lumped;
   if(name=="AbsRowSum")
      return AbsRowSum;
   if(name=="BlkDiag")
      return BlkDiag;
 
   return NotDiag;
}

LinearOp probe(Teuchos::RCP<const Epetra_CrsGraph> &G,const LinearOp & Op){
#ifdef Teko_ENABLE_Isorropia
  Teuchos::ParameterList probeList;
  Prober prober(G,probeList,true);
  Teuchos::RCP<Epetra_CrsMatrix> Mat=rcp(new Epetra_CrsMatrix(Copy,*G));
  Teko::Epetra::EpetraOperatorWrapper Mwrap(Op);
  prober.probe(Mwrap,*Mat);
  return Thyra::epetraLinearOp(Mat);    
#else
  TEUCHOS_TEST_FOR_EXCEPTION(true,std::runtime_error,"Probe requires Isorropia");
#endif
}

double norm_1(const MultiVector & v,std::size_t col)
{
   Teuchos::Array<double> n(v->domain()->dim());
   Thyra::norms_1<double>(*v,n);

   return n[col];
}

double norm_2(const MultiVector & v,std::size_t col)
{
   Teuchos::Array<double> n(v->domain()->dim());
   Thyra::norms_2<double>(*v,n);

   return n[col];
}

void putScalar(const ModifiableLinearOp & op,double scalar) 
{
   try {
      // get Epetra_Operator
      RCP<Epetra_Operator> eOp = Thyra::get_Epetra_Operator(*op);

      // cast it to a CrsMatrix
      RCP<Epetra_CrsMatrix> eCrsOp = rcp_dynamic_cast<Epetra_CrsMatrix>(eOp,true);

     eCrsOp->PutScalar(scalar);
   }
   catch (std::exception & e) {
      RCP<Teuchos::FancyOStream> out = Teuchos::VerboseObjectBase::getDefaultOStream();

      *out << "Teko: putScalar requires an Epetra_CrsMatrix\n";
      *out << "    Could not extract an Epetra_Operator from a \"" << op->description() << std::endl;
      *out << "           OR\n";
      *out << "    Could not cast an Epetra_Operator to a Epetra_CrsMatrix\n";
      *out << std::endl;
      *out << "*** THROWN EXCEPTION ***\n";
      *out << e.what() << std::endl;
      *out << "************************\n";
      
      throw e;
   }
}

void clipLower(MultiVector & v,double lowerBound)
{
   using Teuchos::RCP;
   using Teuchos::rcp_dynamic_cast;

   // cast so entries are accessible
   // RCP<Thyra::SpmdMultiVectorBase<double> > spmdMVec  
   //    = rcp_dynamic_cast<Thyra::DefaultSpmdMultiVector<double> >(v);
   
   for(Thyra::Ordinal i=0;i<v->domain()->dim();i++) {
      RCP<Thyra::SpmdVectorBase<double> > spmdVec  
         = rcp_dynamic_cast<Thyra::SpmdVectorBase<double> >(v->col(i),true);
   
      Teuchos::ArrayRCP<double> values;
      // spmdMVec->getNonconstLocalData(Teuchos::ptrFromRef(values),Teuchos::ptrFromRef(i));
      spmdVec->getNonconstLocalData(Teuchos::ptrFromRef(values));
      for(Teuchos::ArrayRCP<double>::size_type j=0;j<values.size();j++) {
         if(values[j]<lowerBound)
            values[j] = lowerBound;
      }
   }
}

void clipUpper(MultiVector & v,double upperBound)
{
   using Teuchos::RCP;
   using Teuchos::rcp_dynamic_cast;

   // cast so entries are accessible
   // RCP<Thyra::SpmdMultiVectorBase<double> > spmdMVec  
   //   = rcp_dynamic_cast<Thyra::DefaultSpmdMultiVector<double> >(v);
   for(Thyra::Ordinal i=0;i<v->domain()->dim();i++) {
      RCP<Thyra::SpmdVectorBase<double> > spmdVec  
         = rcp_dynamic_cast<Thyra::SpmdVectorBase<double> >(v->col(i),true);
   
      Teuchos::ArrayRCP<double> values;
      // spmdMVec->getNonconstLocalData(Teuchos::ptrFromRef(values),Teuchos::ptrFromRef(i));
      spmdVec->getNonconstLocalData(Teuchos::ptrFromRef(values));
      for(Teuchos::ArrayRCP<double>::size_type j=0;j<values.size();j++) {
         if(values[j]>upperBound)
            values[j] = upperBound;
      }
   }
}

void replaceValue(MultiVector & v,double currentValue,double newValue)
{
   using Teuchos::RCP;
   using Teuchos::rcp_dynamic_cast;

   // cast so entries are accessible
   // RCP<Thyra::SpmdMultiVectorBase<double> > spmdMVec  
   //    = rcp_dynamic_cast<Thyra::SpmdMultiVectorBase<double> >(v,true);
   for(Thyra::Ordinal i=0;i<v->domain()->dim();i++) {
      RCP<Thyra::SpmdVectorBase<double> > spmdVec  
         = rcp_dynamic_cast<Thyra::SpmdVectorBase<double> >(v->col(i),true);
   
      Teuchos::ArrayRCP<double> values;
      // spmdMVec->getNonconstLocalData(Teuchos::ptrFromRef(values),Teuchos::ptrFromRef(i));
      spmdVec->getNonconstLocalData(Teuchos::ptrFromRef(values));
      for(Teuchos::ArrayRCP<double>::size_type j=0;j<values.size();j++) {
         if(values[j]==currentValue)
            values[j] = newValue;
      }
   }
}

void columnAverages(const MultiVector & v,std::vector<double> & averages)
{
   averages.resize(v->domain()->dim());

   // sum over each column
   Thyra::sums<double>(*v,averages);

   // build averages
   Thyra::Ordinal rows = v->range()->dim();
   for(std::size_t i=0;i<averages.size();i++)
      averages[i] = averages[i]/rows;
}

double average(const MultiVector & v)
{
   Thyra::Ordinal rows = v->range()->dim();
   Thyra::Ordinal cols = v->domain()->dim();

   std::vector<double> averages;
   columnAverages(v,averages);

   double sum = 0.0;
   for(std::size_t i=0;i<averages.size();i++)
      sum += averages[i] * rows;

   return sum/(rows*cols);
}

}