Remove tnt/jama

This was used in the past by SCM/PDM, but hasn't been used for a long time now.

30 files changed, 1 insertions, 7248 deletions

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 3e8bca1..3ed3bf3 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -37,12 +37,11 @@ ifeq ($(matlab),yes)
 CPPFLAGS+=-I$(MATLAB_ROOT)/extern/include -DMATLAB_MEX_FILE
 endif
 
-TNT_CPPFLAGS=@TNT_CPPFLAGS@
 BOOST_CPPFLAGS=
 BOOST_LDFLAGS=
 
 
-CPPFLAGS+=$(TNT_CPPFLAGS) $(BOOST_CPPFLAGS)
+CPPFLAGS+=$(BOOST_CPPFLAGS)
 LDFLAGS+=$(BOOST_LDFLAGS)
 
 
diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index f58ad0e..de2b2f1 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -46,19 +46,6 @@ AC_LANG([C++])
 dnl Use iostream to check if the C++ compiler works
 AC_CHECK_HEADER(iostream, , AC_MSG_ERROR([No working c++ compiler found]))
 
-dnl TODO: Use ../../lib/include instead of .../tnt once all other
-dnl       libraries have been moved out of SVN
-TNT_CPPFLAGS="-I../../lib/include/tnt -DJAMA_NO_SUBDIR"
-CPPFLAGS="$CPPFLAGS $TNT_CPPFLAGS"
-AC_CHECK_HEADER(tnt.h, HAVETNT=yes, HAVETNT=no)
-AC_CHECK_HEADER(jama_lu.h, HAVEJAMA=yes, HAVEJAMA=no)
-
-if test x$HAVETNT = xno -o x$HAVEJAMA = xno; then
-  AC_MSG_ERROR([tnt or jama not found])
-fi
-AC_SUBST(TNT_CPPFLAGS)
-
-
 
 # boost-unit-test-framework
 
diff --git a/include/astra/jama_wrapper.h b/include/astra/jama_wrapper.h
deleted file mode 100644
index 2fbdef8..0000000
--- a/include/astra/jama_wrapper.h
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright 2012 iMinds-Vision Lab, University of Antwerp
-
-Contact: astra@ua.ac.be
-Website: http://astra.ua.ac.be
-
-
-This file is part of the
-All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-
-The ASTRA Toolbox is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-$Id$
-*/
-
-// Wrapper include for jama header files
-
-#ifdef JAMA_NO_SUBDIR
-#include "jama_lu.h"
-#else
-#include <tnt/jama_lu.h>
-#endif
diff --git a/lib/include/tnt/jama_cholesky.h b/lib/include/tnt/jama_cholesky.h
deleted file mode 100644
index 371d2f7..0000000
--- a/lib/include/tnt/jama_cholesky.h
+++ /dev/null
@@ -1,258 +0,0 @@
-#ifndef JAMA_CHOLESKY_H
-#define JAMA_CHOLESKY_H
-
-#include "math.h"
-	/* needed for sqrt() below. */
-
-
-namespace JAMA
-{
-
-using namespace TNT;
-
-/** 
-   <P>
-   For a symmetric, positive definite matrix A, this function
-   computes the Cholesky factorization, i.e. it computes a lower 
-   triangular matrix L such that A = L*L'.
-   If the matrix is not symmetric or positive definite, the function
-   computes only a partial decomposition.  This can be tested with
-   the is_spd() flag.
-
-   <p>Typical usage looks like:
-   <pre>
-	Array2D<double> A(n,n);
-	Array2D<double> L;
-
-	 ... 
-
-	Cholesky<double> chol(A);
-
-	if (chol.is_spd())
-		L = chol.getL();
-		
-  	else
-		cout << "factorization was not complete.\n";
-
-	</pre>
-
-
-   <p>
-	(Adapted from JAMA, a Java Matrix Library, developed by jointly 
-	by the Mathworks and NIST; see  http://math.nist.gov/javanumerics/jama).
-
-   */
-
-template <class Real>
-class Cholesky
-{
-	Array2D<Real> L_;		// lower triangular factor
-	int isspd;				// 1 if matrix to be factored was SPD
-
-public:
-
-	Cholesky();
-	Cholesky(const Array2D<Real> &A);
-	Array2D<Real> getL() const;
-	Array1D<Real> solve(const Array1D<Real> &B);
-	Array2D<Real> solve(const Array2D<Real> &B);
-	int is_spd() const;
-
-};
-
-template <class Real>
-Cholesky<Real>::Cholesky() : L_(0,0), isspd(0) {}
-
-/**
-	@return 1, if original matrix to be factored was symmetric 
-		positive-definite (SPD).
-*/
-template <class Real>
-int Cholesky<Real>::is_spd() const
-{
-	return isspd;
-}
-
-/**
-	@return the lower triangular factor, L, such that L*L'=A.
-*/
-template <class Real>
-Array2D<Real> Cholesky<Real>::getL() const
-{
-	return L_;
-}
-
-/**
-	Constructs a lower triangular matrix L, such that L*L'= A.
-	If A is not symmetric positive-definite (SPD), only a
-	partial factorization is performed.  If is_spd()
-	evalutate true (1) then the factorizaiton was successful.
-*/
-template <class Real>
-Cholesky<Real>::Cholesky(const Array2D<Real> &A)
-{
-
-
-   	int m = A.dim1();
-	int n = A.dim2();
-	
-	isspd = (m == n);
-
-	if (m != n)
-	{
-		L_ = Array2D<Real>(0,0);
-		return;
-	}
-
-	L_ = Array2D<Real>(n,n);
-
-
-      // Main loop.
-     for (int j = 0; j < n; j++) 
-	 {
-        Real d(0.0);
-        for (int k = 0; k < j; k++) 
-		{
-            Real s(0.0);
-            for (int i = 0; i < k; i++) 
-			{
-               s += L_[k][i]*L_[j][i];
-            }
-            L_[j][k] = s = (A[j][k] - s)/L_[k][k];
-            d = d + s*s;
-            isspd = isspd && (A[k][j] == A[j][k]); 
-         }
-         d = A[j][j] - d;
-         isspd = isspd && (d > 0.0);
-         L_[j][j] = sqrt(d > 0.0 ? d : 0.0);
-         for (int k = j+1; k < n; k++) 
-		 {
-            L_[j][k] = 0.0;
-         }
-	}
-}
-
-/**
-
-	Solve a linear system A*x = b, using the previously computed
-	cholesky factorization of A: L*L'.
-
-   @param  B   A Matrix with as many rows as A and any number of columns.
-   @return     x so that L*L'*x = b.  If b is nonconformat, or if A
-   				was not symmetric posidtive definite, a null (0x0)
-   						array is returned.
-*/
-template <class Real>
-Array1D<Real> Cholesky<Real>::solve(const Array1D<Real> &b)
-{
-	int n = L_.dim1();
-	if (b.dim1() != n)
-		return Array1D<Real>();
-
-
-	Array1D<Real> x = b.copy();
-
-
-      // Solve L*y = b;
-      for (int k = 0; k < n; k++) 
-	  {
-         for (int i = 0; i < k; i++) 
-               x[k] -= x[i]*L_[k][i];
-		 x[k] /= L_[k][k];
-		
-      }
-
-      // Solve L'*X = Y;
-      for (int k = n-1; k >= 0; k--) 
-	  {
-         for (int i = k+1; i < n; i++) 
-               x[k] -= x[i]*L_[i][k];
-         x[k] /= L_[k][k];
-      }
-
-	return x;
-}
-
-
-/**
-
-	Solve a linear system A*X = B, using the previously computed
-	cholesky factorization of A: L*L'.
-
-   @param  B   A Matrix with as many rows as A and any number of columns.
-   @return     X so that L*L'*X = B.  If B is nonconformat, or if A
-   				was not symmetric posidtive definite, a null (0x0)
-   						array is returned.
-*/
-template <class Real>
-Array2D<Real> Cholesky<Real>::solve(const Array2D<Real> &B)
-{
-	int n = L_.dim1();
-	if (B.dim1() != n)
-		return Array2D<Real>();
-
-
-	Array2D<Real> X = B.copy();
-	int nx = B.dim2();
-
-// Cleve's original code
-#if 0
-      // Solve L*Y = B;
-      for (int k = 0; k < n; k++) {
-         for (int i = k+1; i < n; i++) {
-            for (int j = 0; j < nx; j++) {
-               X[i][j] -= X[k][j]*L_[k][i];
-            }
-         }
-         for (int j = 0; j < nx; j++) {
-            X[k][j] /= L_[k][k];
-         }
-      }
-
-      // Solve L'*X = Y;
-      for (int k = n-1; k >= 0; k--) {
-         for (int j = 0; j < nx; j++) {
-            X[k][j] /= L_[k][k];
-         }
-         for (int i = 0; i < k; i++) {
-            for (int j = 0; j < nx; j++) {
-               X[i][j] -= X[k][j]*L_[k][i];
-            }
-         }
-      }
-#endif
-
-
-      // Solve L*y = b;
-  	  for (int j=0; j< nx; j++)
-	  {
-      	for (int k = 0; k < n; k++) 
-		{
-			for (int i = 0; i < k; i++) 
-               X[k][j] -= X[i][j]*L_[k][i];
-		    X[k][j] /= L_[k][k];
-		 }
-      }
-
-      // Solve L'*X = Y;
-     for (int j=0; j<nx; j++)
-	 {
-      	for (int k = n-1; k >= 0; k--) 
-	  	{
-         	for (int i = k+1; i < n; i++) 
-               X[k][j] -= X[i][j]*L_[i][k];
-         	X[k][j] /= L_[k][k];
-		}
-      }
-
-
-
-	return X;
-}
-
-
-}
-// namespace JAMA
-
-#endif
-// JAMA_CHOLESKY_H
diff --git a/lib/include/tnt/jama_eig.h b/lib/include/tnt/jama_eig.h
deleted file mode 100644
index 8e3572f..0000000
--- a/lib/include/tnt/jama_eig.h
+++ /dev/null
@@ -1,1034 +0,0 @@
-#ifndef JAMA_EIG_H
-#define JAMA_EIG_H
-
-
-#include "tnt_array1d.h"
-#include "tnt_array2d.h"
-#include "tnt_math_utils.h"
-
-#include <algorithm>
-// for min(), max() below
-
-#include <cmath>
-// for abs() below
-
-using namespace TNT;
-using namespace std;
-
-// Modification by Willem Jan Palenstijn, 2010-03-11:
-// Use std::min() instead of min(), std::max() instead of max()
-
-
-namespace JAMA
-{
-
-/** 
-
-    Computes eigenvalues and eigenvectors of a real (non-complex)
-    matrix. 
-<P>
-    If A is symmetric, then A = V*D*V' where the eigenvalue matrix D is
-    diagonal and the eigenvector matrix V is orthogonal. That is,
-	the diagonal values of D are the eigenvalues, and
-    V*V' = I, where I is the identity matrix.  The columns of V 
-    represent the eigenvectors in the sense that A*V = V*D.
-    
-<P>
-    If A is not symmetric, then the eigenvalue matrix D is block diagonal
-    with the real eigenvalues in 1-by-1 blocks and any complex eigenvalues,
-    a + i*b, in 2-by-2 blocks, [a, b; -b, a].  That is, if the complex
-    eigenvalues look like
-<pre>
-
-          u + iv     .        .          .      .    .
-            .      u - iv     .          .      .    .
-            .        .      a + ib       .      .    .
-            .        .        .        a - ib   .    .
-            .        .        .          .      x    .
-            .        .        .          .      .    y
-</pre>
-        then D looks like
-<pre>
-
-            u        v        .          .      .    .
-           -v        u        .          .      .    . 
-            .        .        a          b      .    .
-            .        .       -b          a      .    .
-            .        .        .          .      x    .
-            .        .        .          .      .    y
-</pre>
-    This keeps V a real matrix in both symmetric and non-symmetric
-    cases, and A*V = V*D.
-    
-    
-    
-    <p>
-    The matrix V may be badly
-    conditioned, or even singular, so the validity of the equation
-    A = V*D*inverse(V) depends upon the condition number of V.
-
-   <p>
-	(Adapted from JAMA, a Java Matrix Library, developed by jointly 
-	by the Mathworks and NIST; see  http://math.nist.gov/javanumerics/jama).
-**/
-
-template <class Real>
-class Eigenvalue
-{
-
-
-   /** Row and column dimension (square matrix).  */
-    int n;
-
-   int issymmetric; /* boolean*/
-
-   /** Arrays for internal storage of eigenvalues. */
-
-   TNT::Array1D<Real> d;         /* real part */
-   TNT::Array1D<Real> e;         /* img part */
-
-   /** Array for internal storage of eigenvectors. */
-    TNT::Array2D<Real> V;
-
-   /** Array for internal storage of nonsymmetric Hessenberg form.
-   @serial internal storage of nonsymmetric Hessenberg form.
-   */
-   TNT::Array2D<Real> H;
-   
-
-   /** Working storage for nonsymmetric algorithm.
-   @serial working storage for nonsymmetric algorithm.
-   */
-   TNT::Array1D<Real> ort;
-
-
-   // Symmetric Householder reduction to tridiagonal form.
-
-   void tred2() {
-
-   //  This is derived from the Algol procedures tred2 by
-   //  Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
-   //  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
-   //  Fortran subroutine in EISPACK.
-
-      for (int j = 0; j < n; j++) {
-         d[j] = V[n-1][j];
-      }
-
-      // Householder reduction to tridiagonal form.
-   
-      for (int i = n-1; i > 0; i--) {
-   
-         // Scale to avoid under/overflow.
-   
-         Real scale = 0.0;
-         Real h = 0.0;
-         for (int k = 0; k < i; k++) {
-            scale = scale + abs(d[k]);
-         }
-         if (scale == 0.0) {
-            e[i] = d[i-1];
-            for (int j = 0; j < i; j++) {
-               d[j] = V[i-1][j];
-               V[i][j] = 0.0;
-               V[j][i] = 0.0;
-            }
-         } else {
-   
-            // Generate Householder vector.
-   
-            for (int k = 0; k < i; k++) {
-               d[k] /= scale;
-               h += d[k] * d[k];
-            }
-            Real f = d[i-1];
-            Real g = sqrt(h);
-            if (f > 0) {
-               g = -g;
-            }
-            e[i] = scale * g;
-            h = h - f * g;
-            d[i-1] = f - g;
-            for (int j = 0; j < i; j++) {
-               e[j] = 0.0;
-            }
-   
-            // Apply similarity transformation to remaining columns.
-   
-            for (int j = 0; j < i; j++) {
-               f = d[j];
-               V[j][i] = f;
-               g = e[j] + V[j][j] * f;
-               for (int k = j+1; k <= i-1; k++) {
-                  g += V[k][j] * d[k];
-                  e[k] += V[k][j] * f;
-               }
-               e[j] = g;
-            }
-            f = 0.0;
-            for (int j = 0; j < i; j++) {
-               e[j] /= h;
-               f += e[j] * d[j];
-            }
-            Real hh = f / (h + h);
-            for (int j = 0; j < i; j++) {
-               e[j] -= hh * d[j];
-            }
-            for (int j = 0; j < i; j++) {
-               f = d[j];
-               g = e[j];
-               for (int k = j; k <= i-1; k++) {
-                  V[k][j] -= (f * e[k] + g * d[k]);
-               }
-               d[j] = V[i-1][j];
-               V[i][j] = 0.0;
-            }
-         }
-         d[i] = h;
-      }
-   
-      // Accumulate transformations.
-   
-      for (int i = 0; i < n-1; i++) {
-         V[n-1][i] = V[i][i];
-         V[i][i] = 1.0;
-         Real h = d[i+1];
-         if (h != 0.0) {
-            for (int k = 0; k <= i; k++) {
-               d[k] = V[k][i+1] / h;
-            }
-            for (int j = 0; j <= i; j++) {
-               Real g = 0.0;
-               for (int k = 0; k <= i; k++) {
-                  g += V[k][i+1] * V[k][j];
-               }
-               for (int k = 0; k <= i; k++) {
-                  V[k][j] -= g * d[k];
-               }
-            }
-         }
-         for (int k = 0; k <= i; k++) {
-            V[k][i+1] = 0.0;
-         }
-      }
-      for (int j = 0; j < n; j++) {
-         d[j] = V[n-1][j];
-         V[n-1][j] = 0.0;
-      }
-      V[n-1][n-1] = 1.0;
-      e[0] = 0.0;
-   } 
-
-   // Symmetric tridiagonal QL algorithm.
-   
-   void tql2 () {
-
-   //  This is derived from the Algol procedures tql2, by
-   //  Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
-   //  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
-   //  Fortran subroutine in EISPACK.
-   
-      for (int i = 1; i < n; i++) {
-         e[i-1] = e[i];
-      }
-      e[n-1] = 0.0;
-   
-      Real f = 0.0;
-      Real tst1 = 0.0;
-      Real eps = pow(2.0,-52.0);
-      for (int l = 0; l < n; l++) {
-
-         // Find small subdiagonal element
-   
-         tst1 = std::max(tst1,abs(d[l]) + abs(e[l]));
-         int m = l;
-
-        // Original while-loop from Java code
-         while (m < n) {
-            if (abs(e[m]) <= eps*tst1) {
-               break;
-            }
-            m++;
-         }
-
-   
-         // If m == l, d[l] is an eigenvalue,
-         // otherwise, iterate.
-   
-         if (m > l) {
-            int iter = 0;
-            do {
-               iter = iter + 1;  // (Could check iteration count here.)
-   
-               // Compute implicit shift
-   
-               Real g = d[l];
-               Real p = (d[l+1] - g) / (2.0 * e[l]);
-               Real r = hypot(p,1.0);
-               if (p < 0) {
-                  r = -r;
-               }
-               d[l] = e[l] / (p + r);
-               d[l+1] = e[l] * (p + r);
-               Real dl1 = d[l+1];
-               Real h = g - d[l];
-               for (int i = l+2; i < n; i++) {
-                  d[i] -= h;
-               }
-               f = f + h;
-   
-               // Implicit QL transformation.
-   
-               p = d[m];
-               Real c = 1.0;
-               Real c2 = c;
-               Real c3 = c;
-               Real el1 = e[l+1];
-               Real s = 0.0;
-               Real s2 = 0.0;
-               for (int i = m-1; i >= l; i--) {
-                  c3 = c2;
-                  c2 = c;
-                  s2 = s;
-                  g = c * e[i];
-                  h = c * p;
-                  r = hypot(p,e[i]);
-                  e[i+1] = s * r;
-                  s = e[i] / r;
-                  c = p / r;
-                  p = c * d[i] - s * g;
-                  d[i+1] = h + s * (c * g + s * d[i]);
-   
-                  // Accumulate transformation.
-   
-                  for (int k = 0; k < n; k++) {
-                     h = V[k][i+1];
-                     V[k][i+1] = s * V[k][i] + c * h;
-                     V[k][i] = c * V[k][i] - s * h;
-                  }
-               }
-               p = -s * s2 * c3 * el1 * e[l] / dl1;
-               e[l] = s * p;
-               d[l] = c * p;
-   
-               // Check for convergence.
-   
-            } while (abs(e[l]) > eps*tst1);
-         }
-         d[l] = d[l] + f;
-         e[l] = 0.0;
-      }
-     
-      // Sort eigenvalues and corresponding vectors.
-   
-      for (int i = 0; i < n-1; i++) {
-         int k = i;
-         Real p = d[i];
-         for (int j = i+1; j < n; j++) {
-            if (d[j] < p) {
-               k = j;
-               p = d[j];
-            }
-         }
-         if (k != i) {
-            d[k] = d[i];
-            d[i] = p;
-            for (int j = 0; j < n; j++) {
-               p = V[j][i];
-               V[j][i] = V[j][k];
-               V[j][k] = p;
-            }
-         }
-      }
-   }
-
-   // Nonsymmetric reduction to Hessenberg form.
-
-   void orthes () {
-   
-      //  This is derived from the Algol procedures orthes and ortran,
-      //  by Martin and Wilkinson, Handbook for Auto. Comp.,
-      //  Vol.ii-Linear Algebra, and the corresponding
-      //  Fortran subroutines in EISPACK.
-   
-      int low = 0;
-      int high = n-1;
-   
-      for (int m = low+1; m <= high-1; m++) {
-   
-         // Scale column.
-   
-         Real scale = 0.0;
-         for (int i = m; i <= high; i++) {
-            scale = scale + abs(H[i][m-1]);
-         }
-         if (scale != 0.0) {
-   
-            // Compute Householder transformation.
-   
-            Real h = 0.0;
-            for (int i = high; i >= m; i--) {
-               ort[i] = H[i][m-1]/scale;
-               h += ort[i] * ort[i];
-            }
-            Real g = sqrt(h);
-            if (ort[m] > 0) {
-               g = -g;
-            }
-            h = h - ort[m] * g;
-            ort[m] = ort[m] - g;
-   
-            // Apply Householder similarity transformation
-            // H = (I-u*u'/h)*H*(I-u*u')/h)
-   
-            for (int j = m; j < n; j++) {
-               Real f = 0.0;
-               for (int i = high; i >= m; i--) {
-                  f += ort[i]*H[i][j];
-               }
-               f = f/h;
-               for (int i = m; i <= high; i++) {
-                  H[i][j] -= f*ort[i];
-               }
-           }
-   
-           for (int i = 0; i <= high; i++) {
-               Real f = 0.0;
-               for (int j = high; j >= m; j--) {
-                  f += ort[j]*H[i][j];
-               }
-               f = f/h;
-               for (int j = m; j <= high; j++) {
-                  H[i][j] -= f*ort[j];
-               }
-            }
-            ort[m] = scale*ort[m];
-            H[m][m-1] = scale*g;
-         }
-      }
-   
-      // Accumulate transformations (Algol's ortran).
-
-      for (int i = 0; i < n; i++) {
-         for (int j = 0; j < n; j++) {
-            V[i][j] = (i == j ? 1.0 : 0.0);
-         }
-      }
-
-      for (int m = high-1; m >= low+1; m--) {
-         if (H[m][m-1] != 0.0) {
-            for (int i = m+1; i <= high; i++) {
-               ort[i] = H[i][m-1];
-            }
-            for (int j = m; j <= high; j++) {
-               Real g = 0.0;
-               for (int i = m; i <= high; i++) {
-                  g += ort[i] * V[i][j];
-               }
-               // Double division avoids possible underflow
-               g = (g / ort[m]) / H[m][m-1];
-               for (int i = m; i <= high; i++) {
-                  V[i][j] += g * ort[i];
-               }
-            }
-         }
-      }
-   }
-
-
-   // Complex scalar division.
-
-   Real cdivr, cdivi;
-   void cdiv(Real xr, Real xi, Real yr, Real yi) {
-      Real r,d;
-      if (abs(yr) > abs(yi)) {
-         r = yi/yr;
-         d = yr + r*yi;
-         cdivr = (xr + r*xi)/d;
-         cdivi = (xi - r*xr)/d;
-      } else {
-         r = yr/yi;
-         d = yi + r*yr;
-         cdivr = (r*xr + xi)/d;
-         cdivi = (r*xi - xr)/d;
-      }
-   }
-
-
-   // Nonsymmetric reduction from Hessenberg to real Schur form.
-
-   void hqr2 () {
-   
-      //  This is derived from the Algol procedure hqr2,
-      //  by Martin and Wilkinson, Handbook for Auto. Comp.,
-      //  Vol.ii-Linear Algebra, and the corresponding
-      //  Fortran subroutine in EISPACK.
-   
-      // Initialize
-   
-      int nn = this->n;
-      int n = nn-1;
-      int low = 0;
-      int high = nn-1;
-      Real eps = pow(2.0,-52.0);
-      Real exshift = 0.0;
-      Real p=0,q=0,r=0,s=0,z=0,t,w,x,y;
-   
-      // Store roots isolated by balanc and compute matrix norm
-   
-      Real norm = 0.0;
-      for (int i = 0; i < nn; i++) {
-         if ((i < low) || (i > high)) {
-            d[i] = H[i][i];
-            e[i] = 0.0;
-         }
-         for (int j = std::max(i-1,0); j < nn; j++) {
-            norm = norm + abs(H[i][j]);
-         }
-      }
-   
-      // Outer loop over eigenvalue index
-   
-      int iter = 0;
-      while (n >= low) {
-   
-         // Look for single small sub-diagonal element
-   
-         int l = n;
-         while (l > low) {
-            s = abs(H[l-1][l-1]) + abs(H[l][l]);
-            if (s == 0.0) {
-               s = norm;
-            }
-            if (abs(H[l][l-1]) < eps * s) {
-               break;
-            }
-            l--;
-         }
-       
-         // Check for convergence
-         // One root found
-   
-         if (l == n) {
-            H[n][n] = H[n][n] + exshift;
-            d[n] = H[n][n];
-            e[n] = 0.0;
-            n--;
-            iter = 0;
-   
-         // Two roots found
-   
-         } else if (l == n-1) {
-            w = H[n][n-1] * H[n-1][n];
-            p = (H[n-1][n-1] - H[n][n]) / 2.0;
-            q = p * p + w;
-            z = sqrt(abs(q));
-            H[n][n] = H[n][n] + exshift;
-            H[n-1][n-1] = H[n-1][n-1] + exshift;
-            x = H[n][n];
-   
-            // Real pair
-   
-            if (q >= 0) {
-               if (p >= 0) {
-                  z = p + z;
-               } else {
-                  z = p - z;
-               }
-               d[n-1] = x + z;
-               d[n] = d[n-1];
-               if (z != 0.0) {
-                  d[n] = x - w / z;
-               }
-               e[n-1] = 0.0;
-               e[n] = 0.0;
-               x = H[n][n-1];
-               s = abs(x) + abs(z);
-               p = x / s;
-               q = z / s;
-               r = sqrt(p * p+q * q);
-               p = p / r;
-               q = q / r;
-   
-               // Row modification
-   
-               for (int j = n-1; j < nn; j++) {
-                  z = H[n-1][j];
-                  H[n-1][j] = q * z + p * H[n][j];
-                  H[n][j] = q * H[n][j] - p * z;
-               }
-   
-               // Column modification
-   
-               for (int i = 0; i <= n; i++) {
-                  z = H[i][n-1];
-                  H[i][n-1] = q * z + p * H[i][n];
-                  H[i][n] = q * H[i][n] - p * z;
-               }
-   
-               // Accumulate transformations
-   
-               for (int i = low; i <= high; i++) {
-                  z = V[i][n-1];
-                  V[i][n-1] = q * z + p * V[i][n];
-                  V[i][n] = q * V[i][n] - p * z;
-               }
-   
-            // Complex pair
-   
-            } else {
-               d[n-1] = x + p;
-               d[n] = x + p;
-               e[n-1] = z;
-               e[n] = -z;
-            }
-            n = n - 2;
-            iter = 0;
-   
-         // No convergence yet
-   
-         } else {
-   
-            // Form shift
-   
-            x = H[n][n];
-            y = 0.0;
-            w = 0.0;
-            if (l < n) {
-               y = H[n-1][n-1];
-               w = H[n][n-1] * H[n-1][n];
-            }
-   
-            // Wilkinson's original ad hoc shift
-   
-            if (iter == 10) {
-               exshift += x;
-               for (int i = low; i <= n; i++) {
-                  H[i][i] -= x;
-               }
-               s = abs(H[n][n-1]) + abs(H[n-1][n-2]);
-               x = y = 0.75 * s;
-               w = -0.4375 * s * s;
-            }
-
-            // MATLAB's new ad hoc shift
-
-            if (iter == 30) {
-                s = (y - x) / 2.0;
-                s = s * s + w;
-                if (s > 0) {
-                    s = sqrt(s);
-                    if (y < x) {
-                       s = -s;
-                    }
-                    s = x - w / ((y - x) / 2.0 + s);
-                    for (int i = low; i <= n; i++) {
-                       H[i][i] -= s;
-                    }
-                    exshift += s;
-                    x = y = w = 0.964;
-                }
-            }
-   
-            iter = iter + 1;   // (Could check iteration count here.)
-   
-            // Look for two consecutive small sub-diagonal elements
-   
-            int m = n-2;
-            while (m >= l) {
-               z = H[m][m];
-               r = x - z;
-               s = y - z;
-               p = (r * s - w) / H[m+1][m] + H[m][m+1];
-               q = H[m+1][m+1] - z - r - s;
-               r = H[m+2][m+1];
-               s = abs(p) + abs(q) + abs(r);
-               p = p / s;
-               q = q / s;
-               r = r / s;
-               if (m == l) {
-                  break;
-               }
-               if (abs(H[m][m-1]) * (abs(q) + abs(r)) <
-                  eps * (abs(p) * (abs(H[m-1][m-1]) + abs(z) +
-                  abs(H[m+1][m+1])))) {
-                     break;
-               }
-               m--;
-            }
-   
-            for (int i = m+2; i <= n; i++) {
-               H[i][i-2] = 0.0;
-               if (i > m+2) {
-                  H[i][i-3] = 0.0;
-               }
-            }
-   
-            // Double QR step involving rows l:n and columns m:n
-   
-            for (int k = m; k <= n-1; k++) {
-               int notlast = (k != n-1);
-               if (k != m) {
-                  p = H[k][k-1];
-                  q = H[k+1][k-1];
-                  r = (notlast ? H[k+2][k-1] : 0.0);
-                  x = abs(p) + abs(q) + abs(r);
-                  if (x != 0.0) {
-                     p = p / x;
-                     q = q / x;
-                     r = r / x;
-                  }
-               }
-               if (x == 0.0) {
-                  break;
-               }
-               s = sqrt(p * p + q * q + r * r);
-               if (p < 0) {
-                  s = -s;
-               }
-               if (s != 0) {
-                  if (k != m) {
-                     H[k][k-1] = -s * x;
-                  } else if (l != m) {
-                     H[k][k-1] = -H[k][k-1];
-                  }
-                  p = p + s;
-                  x = p / s;
-                  y = q / s;
-                  z = r / s;
-                  q = q / p;
-                  r = r / p;
-   
-                  // Row modification
-   
-                  for (int j = k; j < nn; j++) {
-                     p = H[k][j] + q * H[k+1][j];
-                     if (notlast) {
-                        p = p + r * H[k+2][j];
-                        H[k+2][j] = H[k+2][j] - p * z;
-                     }
-                     H[k][j] = H[k][j] - p * x;
-                     H[k+1][j] = H[k+1][j] - p * y;
-                  }
-   
-                  // Column modification
-   
-                  for (int i = 0; i <= std::min(n,k+3); i++) {
-                     p = x * H[i][k] + y * H[i][k+1];
-                     if (notlast) {
-                        p = p + z * H[i][k+2];
-                        H[i][k+2] = H[i][k+2] - p * r;
-                     }
-                     H[i][k] = H[i][k] - p;
-                     H[i][k+1] = H[i][k+1] - p * q;
-                  }
-   
-                  // Accumulate transformations
-   
-                  for (int i = low; i <= high; i++) {
-                     p = x * V[i][k] + y * V[i][k+1];
-                     if (notlast) {
-                        p = p + z * V[i][k+2];
-                        V[i][k+2] = V[i][k+2] - p * r;
-                     }
-                     V[i][k] = V[i][k] - p;
-                     V[i][k+1] = V[i][k+1] - p * q;
-                  }
-               }  // (s != 0)
-            }  // k loop
-         }  // check convergence
-      }  // while (n >= low)
-      
-      // Backsubstitute to find vectors of upper triangular form
-
-      if (norm == 0.0) {
-         return;
-      }
-   
-      for (n = nn-1; n >= 0; n--) {
-         p = d[n];
-         q = e[n];
-   
-         // Real vector
-   
-         if (q == 0) {
-            int l = n;
-            H[n][n] = 1.0;
-            for (int i = n-1; i >= 0; i--) {
-               w = H[i][i] - p;
-               r = 0.0;
-               for (int j = l; j <= n; j++) {
-                  r = r + H[i][j] * H[j][n];
-               }
-               if (e[i] < 0.0) {
-                  z = w;
-                  s = r;
-               } else {
-                  l = i;
-                  if (e[i] == 0.0) {
-                     if (w != 0.0) {
-                        H[i][n] = -r / w;
-                     } else {
-                        H[i][n] = -r / (eps * norm);
-                     }
-   
-                  // Solve real equations
-   
-                  } else {
-                     x = H[i][i+1];
-                     y = H[i+1][i];
-                     q = (d[i] - p) * (d[i] - p) + e[i] * e[i];
-                     t = (x * s - z * r) / q;
-                     H[i][n] = t;
-                     if (abs(x) > abs(z)) {
-                        H[i+1][n] = (-r - w * t) / x;
-                     } else {
-                        H[i+1][n] = (-s - y * t) / z;
-                     }
-                  }
-   
-                  // Overflow control
-   
-                  t = abs(H[i][n]);
-                  if ((eps * t) * t > 1) {
-                     for (int j = i; j <= n; j++) {
-                        H[j][n] = H[j][n] / t;
-                     }
-                  }
-               }
-            }
-   
-         // Complex vector
-   
-         } else if (q < 0) {
-            int l = n-1;
-
-            // Last vector component imaginary so matrix is triangular
-   
-            if (abs(H[n][n-1]) > abs(H[n-1][n])) {
-               H[n-1][n-1] = q / H[n][n-1];
-               H[n-1][n] = -(H[n][n] - p) / H[n][n-1];
-            } else {
-               cdiv(0.0,-H[n-1][n],H[n-1][n-1]-p,q);
-               H[n-1][n-1] = cdivr;
-               H[n-1][n] = cdivi;
-            }
-            H[n][n-1] = 0.0;
-            H[n][n] = 1.0;
-            for (int i = n-2; i >= 0; i--) {
-               Real ra,sa,vr,vi;
-               ra = 0.0;
-               sa = 0.0;
-               for (int j = l; j <= n; j++) {
-                  ra = ra + H[i][j] * H[j][n-1];
-                  sa = sa + H[i][j] * H[j][n];
-               }
-               w = H[i][i] - p;
-   
-               if (e[i] < 0.0) {
-                  z = w;
-                  r = ra;
-                  s = sa;
-               } else {
-                  l = i;
-                  if (e[i] == 0) {
-                     cdiv(-ra,-sa,w,q);
-                     H[i][n-1] = cdivr;
-                     H[i][n] = cdivi;
-                  } else {
-   
-                     // Solve complex equations
-   
-                     x = H[i][i+1];
-                     y = H[i+1][i];
-                     vr = (d[i] - p) * (d[i] - p) + e[i] * e[i] - q * q;
-                     vi = (d[i] - p) * 2.0 * q;
-                     if ((vr == 0.0) && (vi == 0.0)) {
-                        vr = eps * norm * (abs(w) + abs(q) +
-                        abs(x) + abs(y) + abs(z));
-                     }
-                     cdiv(x*r-z*ra+q*sa,x*s-z*sa-q*ra,vr,vi);
-                     H[i][n-1] = cdivr;
-                     H[i][n] = cdivi;
-                     if (abs(x) > (abs(z) + abs(q))) {
-                        H[i+1][n-1] = (-ra - w * H[i][n-1] + q * H[i][n]) / x;
-                        H[i+1][n] = (-sa - w * H[i][n] - q * H[i][n-1]) / x;
-                     } else {
-                        cdiv(-r-y*H[i][n-1],-s-y*H[i][n],z,q);
-                        H[i+1][n-1] = cdivr;
-                        H[i+1][n] = cdivi;
-                     }
-                  }
-   
-                  // Overflow control
-
-                  t = std::max(abs(H[i][n-1]),abs(H[i][n]));
-                  if ((eps * t) * t > 1) {
-                     for (int j = i; j <= n; j++) {
-                        H[j][n-1] = H[j][n-1] / t;
-                        H[j][n] = H[j][n] / t;
-                     }
-                  }
-               }
-            }
-         }
-      }
-   
-      // Vectors of isolated roots
-   
-      for (int i = 0; i < nn; i++) {
-         if (i < low || i > high) {
-            for (int j = i; j < nn; j++) {
-               V[i][j] = H[i][j];
-            }
-         }
-      }
-   
-      // Back transformation to get eigenvectors of original matrix
-   
-      for (int j = nn-1; j >= low; j--) {
-         for (int i = low; i <= high; i++) {
-            z = 0.0;
-            for (int k = low; k <= std::min(j,high); k++) {
-               z = z + V[i][k] * H[k][j];
-            }
-            V[i][j] = z;
-         }
-      }
-   }
-
-public:
-
-
-   /** Check for symmetry, then construct the eigenvalue decomposition
-   @param A    Square real (non-complex) matrix
-   */
-
-   Eigenvalue(const TNT::Array2D<Real> &A) {
-      n = A.dim2();
-      V = Array2D<Real>(n,n);
-      d = Array1D<Real>(n);
-      e = Array1D<Real>(n);
-
-      issymmetric = 1;
-      for (int j = 0; (j < n) && issymmetric; j++) {
-         for (int i = 0; (i < n) && issymmetric; i++) {
-            issymmetric = (A[i][j] == A[j][i]);
-         }
-      }
-
-      if (issymmetric) {
-         for (int i = 0; i < n; i++) {
-            for (int j = 0; j < n; j++) {
-               V[i][j] = A[i][j];
-            }
-         }
-   
-         // Tridiagonalize.
-         tred2();
-   
-         // Diagonalize.
-         tql2();
-
-      } else {
-         H = TNT::Array2D<Real>(n,n);
-         ort = TNT::Array1D<Real>(n);
-         
-         for (int j = 0; j < n; j++) {
-            for (int i = 0; i < n; i++) {
-               H[i][j] = A[i][j];
-            }
-         }
-   
-         // Reduce to Hessenberg form.
-         orthes();
-   
-         // Reduce Hessenberg to real Schur form.
-         hqr2();
-      }
-   }
-
-
-   /** Return the eigenvector matrix
-   @return     V
-   */
-
-   void getV (TNT::Array2D<Real> &V_) {
-      V_ = V;
-      return;
-   }
-
-   /** Return the real parts of the eigenvalues
-   @return     real(diag(D))
-   */
-
-   void getRealEigenvalues (TNT::Array1D<Real> &d_) {
-      d_ = d;
-      return ;
-   }
-
-   /** Return the imaginary parts of the eigenvalues
-   in parameter e_.
-
-   @pararm e_: new matrix with imaginary parts of the eigenvalues.
-   */
-   void getImagEigenvalues (TNT::Array1D<Real> &e_) {
-      e_ = e;
-      return;
-   }
-
-   
-/** 
-	Computes the block diagonal eigenvalue matrix.
-    If the original matrix A is not symmetric, then the eigenvalue 
-	matrix D is block diagonal with the real eigenvalues in 1-by-1 
-	blocks and any complex eigenvalues,
-    a + i*b, in 2-by-2 blocks, [a, b; -b, a].  That is, if the complex
-    eigenvalues look like
-<pre>
-
-          u + iv     .        .          .      .    .
-            .      u - iv     .          .      .    .
-            .        .      a + ib       .      .    .
-            .        .        .        a - ib   .    .
-            .        .        .          .      x    .
-            .        .        .          .      .    y
-</pre>
-        then D looks like
-<pre>
-
-            u        v        .          .      .    .
-           -v        u        .          .      .    . 
-            .        .        a          b      .    .
-            .        .       -b          a      .    .
-            .        .        .          .      x    .
-            .        .        .          .      .    y
-</pre>
-    This keeps V a real matrix in both symmetric and non-symmetric
-    cases, and A*V = V*D.
-
-	@param D: upon return, the matrix is filled with the block diagonal 
-	eigenvalue matrix.
-	
-*/
-   void getD (TNT::Array2D<Real> &D) {
-      D = Array2D<Real>(n,n);
-      for (int i = 0; i < n; i++) {
-         for (int j = 0; j < n; j++) {
-            D[i][j] = 0.0;
-         }
-         D[i][i] = d[i];
-         if (e[i] > 0) {
-            D[i][i+1] = e[i];
-         } else if (e[i] < 0) {
-            D[i][i-1] = e[i];
-         }
-      }
-   }
-};
-
-} //namespace JAMA
-
-
-#endif
-// JAMA_EIG_H
diff --git a/lib/include/tnt/jama_lu.h b/lib/include/tnt/jama_lu.h
deleted file mode 100644
index e95b433..0000000
--- a/lib/include/tnt/jama_lu.h
+++ /dev/null
@@ -1,323 +0,0 @@
-#ifndef JAMA_LU_H
-#define JAMA_LU_H
-
-#include "tnt.h"
-#include <algorithm>
-//for min(), max() below
-
-using namespace TNT;
-using namespace std;
-
-
-// Modification by Willem Jan Palenstijn, 2010-03-11:
-// Use std::min() instead of min()
-
-namespace JAMA
-{
-
-   /** LU Decomposition.
-   <P>
-   For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n
-   unit lower triangular matrix L, an n-by-n upper triangular matrix U,
-   and a permutation vector piv of length m so that A(piv,:) = L*U.
-   If m < n, then L is m-by-m and U is m-by-n.
-   <P>
-   The LU decompostion with pivoting always exists, even if the matrix is
-   singular, so the constructor will never fail.  The primary use of the
-   LU decomposition is in the solution of square systems of simultaneous
-   linear equations.  This will fail if isNonsingular() returns false.
-   */
-template <class Real>
-class LU
-{
-
-
-
-   /* Array for internal storage of decomposition.  */
-   Array2D<Real>  LU_;
-   int m, n, pivsign; 
-   Array1D<int> piv;
-
-
-   Array2D<Real> permute_copy(const Array2D<Real> &A, 
-   			const Array1D<int> &piv, int j0, int j1)
-	{
-		int piv_length = piv.dim();
-
-		Array2D<Real> X(piv_length, j1-j0+1);
-
-
-         for (int i = 0; i < piv_length; i++) 
-            for (int j = j0; j <= j1; j++) 
-               X[i][j-j0] = A[piv[i]][j];
-
-		return X;
-	}
-
-   Array1D<Real> permute_copy(const Array1D<Real> &A, 
-   		const Array1D<int> &piv)
-	{
-		int piv_length = piv.dim();
-		if (piv_length != A.dim())
-			return Array1D<Real>();
-
-		Array1D<Real> x(piv_length);
-
-
-         for (int i = 0; i < piv_length; i++) 
-               x[i] = A[piv[i]];
-
-		return x;
-	}
-
-
-	public :
-
-   /** LU Decomposition
-   @param  A   Rectangular matrix
-   @return     LU Decomposition object to access L, U and piv.
-   */
-
-    LU (const Array2D<Real> &A) : LU_(A.copy()), m(A.dim1()), n(A.dim2()), 
-		piv(A.dim1())
-	
-	{
-
-   // Use a "left-looking", dot-product, Crout/Doolittle algorithm.
-
-
-      for (int i = 0; i < m; i++) {
-         piv[i] = i;
-      }
-      pivsign = 1;
-      Real *LUrowi = 0;;
-      Array1D<Real> LUcolj(m);
-
-      // Outer loop.
-
-      for (int j = 0; j < n; j++) {
-
-         // Make a copy of the j-th column to localize references.
-
-         for (int i = 0; i < m; i++) {
-            LUcolj[i] = LU_[i][j];
-         }
-
-         // Apply previous transformations.
-
-         for (int i = 0; i < m; i++) {
-            LUrowi = LU_[i];
-
-            // Most of the time is spent in the following dot product.
-
-            int kmax = std::min(i,j);
-            double s = 0.0;
-            for (int k = 0; k < kmax; k++) {
-               s += LUrowi[k]*LUcolj[k];
-            }
-
-            LUrowi[j] = LUcolj[i] -= s;
-         }
-   
-         // Find pivot and exchange if necessary.
-
-         int p = j;
-         for (int i = j+1; i < m; i++) {
-            if (abs(LUcolj[i]) > abs(LUcolj[p])) {
-               p = i;
-            }
-         }
-         if (p != j) {
-		    int k=0;
-            for (k = 0; k < n; k++) {
-               double t = LU_[p][k]; 
-			   LU_[p][k] = LU_[j][k]; 
-			   LU_[j][k] = t;
-            }
-            k = piv[p]; 
-			piv[p] = piv[j]; 
-			piv[j] = k;
-            pivsign = -pivsign;
-         }
-
-         // Compute multipliers.
-         
-         if ((j < m) && (LU_[j][j] != 0.0)) {
-            for (int i = j+1; i < m; i++) {
-               LU_[i][j] /= LU_[j][j];
-            }
-         }
-      }
-   }
-
-
-   /** Is the matrix nonsingular?
-   @return     1 (true)  if upper triangular factor U (and hence A) 
-   				is nonsingular, 0 otherwise.
-   */
-
-   int isNonsingular () {
-      for (int j = 0; j < n; j++) {
-         if (LU_[j][j] == 0)
-            return 0;
-      }
-      return 1;
-   }
-
-   /** Return lower triangular factor
-   @return     L
-   */
-
-   Array2D<Real> getL () {
-      Array2D<Real> L_(m,n);
-      for (int i = 0; i < m; i++) {
-         for (int j = 0; j < n; j++) {
-            if (i > j) {
-               L_[i][j] = LU_[i][j];
-            } else if (i == j) {
-               L_[i][j] = 1.0;
-            } else {
-               L_[i][j] = 0.0;
-            }
-         }
-      }
-      return L_;
-   }
-
-   /** Return upper triangular factor
-   @return     U portion of LU factorization.
-   */
-
-   Array2D<Real> getU () {
-   	  Array2D<Real> U_(n,n);
-      for (int i = 0; i < n; i++) {
-         for (int j = 0; j < n; j++) {
-            if (i <= j) {
-               U_[i][j] = LU_[i][j];
-            } else {
-               U_[i][j] = 0.0;
-            }
-         }
-      }
-      return U_;
-   }
-
-   /** Return pivot permutation vector
-   @return     piv
-   */
-
-   Array1D<int> getPivot () {
-      return piv;
-   }
-
-
-   /** Compute determinant using LU factors.
-   @return     determinant of A, or 0 if A is not square.
-   */
-
-   Real det () {
-      if (m != n) {
-         return Real(0);
-      }
-      Real d = Real(pivsign);
-      for (int j = 0; j < n; j++) {
-         d *= LU_[j][j];
-      }
-      return d;
-   }
-
-   /** Solve A*X = B
-   @param  B   A Matrix with as many rows as A and any number of columns.
-   @return     X so that L*U*X = B(piv,:), if B is nonconformant, returns
-   					0x0 (null) array.
-   */
-
-   Array2D<Real> solve (const Array2D<Real> &B) 
-   {
-
-	  /* Dimensions: A is mxn, X is nxk, B is mxk */
-      
-      if (B.dim1() != m) {
-	  	return Array2D<Real>(0,0);
-      }
-      if (!isNonsingular()) {
-        return Array2D<Real>(0,0);
-      }
-
-      // Copy right hand side with pivoting
-      int nx = B.dim2();
-
-
-	  Array2D<Real> X = permute_copy(B, piv, 0, nx-1);
-
-      // Solve L*Y = B(piv,:)
-      for (int k = 0; k < n; k++) {
-         for (int i = k+1; i < n; i++) {
-            for (int j = 0; j < nx; j++) {
-               X[i][j] -= X[k][j]*LU_[i][k];
-            }
-         }
-      }
-      // Solve U*X = Y;
-      for (int k = n-1; k >= 0; k--) {
-         for (int j = 0; j < nx; j++) {
-            X[k][j] /= LU_[k][k];
-         }
-         for (int i = 0; i < k; i++) {
-            for (int j = 0; j < nx; j++) {
-               X[i][j] -= X[k][j]*LU_[i][k];
-            }
-         }
-      }
-      return X;
-   }
-
-
-   /** Solve A*x = b, where x and b are vectors of length equal	
-   		to the number of rows in A.
-
-   @param  b   a vector (Array1D> of length equal to the first dimension
-   						of A.
-   @return x a vector (Array1D> so that L*U*x = b(piv), if B is nonconformant,
-   					returns 0x0 (null) array.
-   */
-
-   Array1D<Real> solve (const Array1D<Real> &b) 
-   {
-
-	  /* Dimensions: A is mxn, X is nxk, B is mxk */
-      
-      if (b.dim1() != m) {
-	  	return Array1D<Real>();
-      }
-      if (!isNonsingular()) {
-        return Array1D<Real>();
-      }
-
-
-	  Array1D<Real> x = permute_copy(b, piv);
-
-      // Solve L*Y = B(piv)
-      for (int k = 0; k < n; k++) {
-         for (int i = k+1; i < n; i++) {
-               x[i] -= x[k]*LU_[i][k];
-            }
-         }
-      
-	  // Solve U*X = Y;
-      for (int k = n-1; k >= 0; k--) {
-            x[k] /= LU_[k][k];
-      		for (int i = 0; i < k; i++) 
-            	x[i] -= x[k]*LU_[i][k];
-      }
-     
-
-      return x;
-   }
-
-}; /* class LU */
-
-} /* namespace JAMA */
-
-#endif
-/* JAMA_LU_H */
diff --git a/lib/include/tnt/jama_qr.h b/lib/include/tnt/jama_qr.h
deleted file mode 100644
index 98d37f5..0000000
--- a/lib/include/tnt/jama_qr.h
+++ /dev/null
@@ -1,326 +0,0 @@
-#ifndef JAMA_QR_H
-#define JAMA_QR_H
-
-#include "tnt_array1d.h"
-#include "tnt_array2d.h"
-#include "tnt_math_utils.h"
-
-namespace JAMA
-{
-
-/** 
-<p>
-	Classical QR Decompisition:
-   for an m-by-n matrix A with m >= n, the QR decomposition is an m-by-n
-   orthogonal matrix Q and an n-by-n upper triangular matrix R so that
-   A = Q*R.
-<P>
-   The QR decompostion always exists, even if the matrix does not have
-   full rank, so the constructor will never fail.  The primary use of the
-   QR decomposition is in the least squares solution of nonsquare systems
-   of simultaneous linear equations.  This will fail if isFullRank()
-   returns 0 (false).
-
-<p>
-	The Q and R factors can be retrived via the getQ() and getR()
-	methods. Furthermore, a solve() method is provided to find the
-	least squares solution of Ax=b using the QR factors.  
-
-   <p>
-	(Adapted from JAMA, a Java Matrix Library, developed by jointly 
-	by the Mathworks and NIST; see  http://math.nist.gov/javanumerics/jama).
-*/
-
-template <class Real>
-class QR {
-
-
-   /** Array for internal storage of decomposition.
-   @serial internal array storage.
-   */
-   
-   TNT::Array2D<Real> QR_;
-
-   /** Row and column dimensions.
-   @serial column dimension.
-   @serial row dimension.
-   */
-   int m, n;
-
-   /** Array for internal storage of diagonal of R.
-   @serial diagonal of R.
-   */
-   TNT::Array1D<Real> Rdiag;
-
-
-public:
-	
-/**
-	Create a QR factorization object for A.
-
-	@param A rectangular (m>=n) matrix.
-*/
-	QR(const TNT::Array2D<Real> &A)		/* constructor */
-	{
-      QR_ = A.copy();
-      m = A.dim1();
-      n = A.dim2();
-      Rdiag = TNT::Array1D<Real>(n);
-	  int i=0, j=0, k=0;
-
-      // Main loop.
-      for (k = 0; k < n; k++) {
-         // Compute 2-norm of k-th column without under/overflow.
-         Real nrm = 0;
-         for (i = k; i < m; i++) {
-            nrm = TNT::hypot(nrm,QR_[i][k]);
-         }
-
-         if (nrm != 0.0) {
-            // Form k-th Householder vector.
-            if (QR_[k][k] < 0) {
-               nrm = -nrm;
-            }
-            for (i = k; i < m; i++) {
-               QR_[i][k] /= nrm;
-            }
-            QR_[k][k] += 1.0;
-
-            // Apply transformation to remaining columns.
-            for (j = k+1; j < n; j++) {
-               Real s = 0.0; 
-               for (i = k; i < m; i++) {
-                  s += QR_[i][k]*QR_[i][j];
-               }
-               s = -s/QR_[k][k];
-               for (i = k; i < m; i++) {
-                  QR_[i][j] += s*QR_[i][k];
-               }
-            }
-         }
-         Rdiag[k] = -nrm;
-      }
-   }
-
-
-/**
-	Flag to denote the matrix is of full rank.
-
-	@return 1 if matrix is full rank, 0 otherwise.
-*/
-	int isFullRank() const		
-	{
-      for (int j = 0; j < n; j++) 
-	  {
-         if (Rdiag[j] == 0)
-            return 0;
-      }
-      return 1;
-	}
-	
-	
-
-
-   /** 
-   
-   Retreive the Householder vectors from QR factorization
-   @returns lower trapezoidal matrix whose columns define the reflections
-   */
-
-   TNT::Array2D<Real> getHouseholder (void)  const
-   {
-   	  TNT::Array2D<Real> H(m,n);
-
-	  /* note: H is completely filled in by algorithm, so
-	     initializaiton of H is not necessary.
-	  */
-      for (int i = 0; i < m; i++) 
-	  {
-         for (int j = 0; j < n; j++) 
-		 {
-            if (i >= j) {
-               H[i][j] = QR_[i][j];
-            } else {
-               H[i][j] = 0.0;
-            }
-         }
-      }
-	  return H;
-   }
-
-
-
-   /** Return the upper triangular factor, R, of the QR factorization
-   @return     R
-   */
-
-	TNT::Array2D<Real> getR() const
-	{
-      TNT::Array2D<Real> R(n,n);
-      for (int i = 0; i < n; i++) {
-         for (int j = 0; j < n; j++) {
-            if (i < j) {
-               R[i][j] = QR_[i][j];
-            } else if (i == j) {
-               R[i][j] = Rdiag[i];
-            } else {
-               R[i][j] = 0.0;
-            }
-         }
-      }
-	  return R;
-   }
-	
-	
-
-
-
-   /** 
-   	Generate and return the (economy-sized) orthogonal factor
-   @param     Q the (ecnomy-sized) orthogonal factor (Q*R=A).
-   */
-
-	TNT::Array2D<Real> getQ() const
-	{
-	  int i=0, j=0, k=0;
-
-	  TNT::Array2D<Real> Q(m,n);
-      for (k = n-1; k >= 0; k--) {
-         for (i = 0; i < m; i++) {
-            Q[i][k] = 0.0;
-         }
-         Q[k][k] = 1.0;
-         for (j = k; j < n; j++) {
-            if (QR_[k][k] != 0) {
-               Real s = 0.0;
-               for (i = k; i < m; i++) {
-                  s += QR_[i][k]*Q[i][j];
-               }
-               s = -s/QR_[k][k];
-               for (i = k; i < m; i++) {
-                  Q[i][j] += s*QR_[i][k];
-               }
-            }
-         }
-      }
-	  return Q;
-   }
-
-
-   /** Least squares solution of A*x = b
-   @param B     m-length array (vector).
-   @return x    n-length array (vector) that minimizes the two norm of Q*R*X-B.
-   		If B is non-conformant, or if QR.isFullRank() is false,
-						the routine returns a null (0-length) vector.
-   */
-
-   TNT::Array1D<Real> solve(const TNT::Array1D<Real> &b) const
-   {
-   	  if (b.dim1() != m)		/* arrays must be conformant */
-	  	return TNT::Array1D<Real>();
-
-	  if ( !isFullRank() )		/* matrix is rank deficient */
-	  {
-	  	return TNT::Array1D<Real>();
-	  }
-
-	  TNT::Array1D<Real> x = b.copy();
-
-      // Compute Y = transpose(Q)*b
-      for (int k = 0; k < n; k++) 
-	  {
-            Real s = 0.0; 
-            for (int i = k; i < m; i++) 
-			{
-               s += QR_[i][k]*x[i];
-            }
-            s = -s/QR_[k][k];
-            for (int i = k; i < m; i++) 
-			{
-               x[i] += s*QR_[i][k];
-            }
-      }
-      // Solve R*X = Y;
-      for (int k = n-1; k >= 0; k--) 
-	  {
-         x[k] /= Rdiag[k];
-         for (int i = 0; i < k; i++) {
-               x[i] -= x[k]*QR_[i][k];
-         }
-      }
-
-
-	  /* return n x nx portion of X */
-	  TNT::Array1D<Real> x_(n);
-	  for (int i=0; i<n; i++)
-			x_[i] = x[i];
-
-	  return x_;
-   }
-
-   /** Least squares solution of A*X = B
-   @param B     m x k Array (must conform).
-   @return X     n x k Array that minimizes the two norm of Q*R*X-B. If
-   						B is non-conformant, or if QR.isFullRank() is false,
-						the routine returns a null (0x0) array.
-   */
-
-   TNT::Array2D<Real> solve(const TNT::Array2D<Real> &B) const
-   {
-   	  if (B.dim1() != m)		/* arrays must be conformant */
-	  	return TNT::Array2D<Real>(0,0);
-
-	  if ( !isFullRank() )		/* matrix is rank deficient */
-	  {
-	  	return TNT::Array2D<Real>(0,0);
-	  }
-
-      int nx = B.dim2(); 
-	  TNT::Array2D<Real> X = B.copy();
-	  int i=0, j=0, k=0;
-
-      // Compute Y = transpose(Q)*B
-      for (k = 0; k < n; k++) {
-         for (j = 0; j < nx; j++) {
-            Real s = 0.0; 
-            for (i = k; i < m; i++) {
-               s += QR_[i][k]*X[i][j];
-            }
-            s = -s/QR_[k][k];
-            for (i = k; i < m; i++) {
-               X[i][j] += s*QR_[i][k];
-            }
-         }
-      }
-      // Solve R*X = Y;
-      for (k = n-1; k >= 0; k--) {
-         for (j = 0; j < nx; j++) {
-            X[k][j] /= Rdiag[k];
-         }
-         for (i = 0; i < k; i++) {
-            for (j = 0; j < nx; j++) {
-               X[i][j] -= X[k][j]*QR_[i][k];
-            }
-         }
-      }
-
-
-	  /* return n x nx portion of X */
-	  TNT::Array2D<Real> X_(n,nx);
-	  for (i=0; i<n; i++)
-	  	for (j=0; j<nx; j++)
-			X_[i][j] = X[i][j];
-
-	  return X_;
-   }
-
-
-};
-
-
-}
-// namespace JAMA
-
-#endif
-// JAMA_QR__H
-
diff --git a/lib/include/tnt/jama_svd.h b/lib/include/tnt/jama_svd.h
deleted file mode 100644
index 72ce3a7..0000000
--- a/lib/include/tnt/jama_svd.h
+++ /dev/null
@@ -1,543 +0,0 @@
-#ifndef JAMA_SVD_H
-#define JAMA_SVD_H
-
-
-#include "tnt_array1d.h"
-#include "tnt_array1d_utils.h"
-#include "tnt_array2d.h"
-#include "tnt_array2d_utils.h"
-#include "tnt_math_utils.h"
-
-#include <algorithm>
-// for min(), max() below
-#include <cmath>
-// for abs() below
-
-using namespace TNT;
-using namespace std;
-
-
-// Modification by Willem Jan Palenstijn, 2010-03-11:
-// Use std::min() instead of min(), std::max() instead of max()
-
-
-namespace JAMA
-{
-   /** Singular Value Decomposition.
-   <P>
-   For an m-by-n matrix A with m >= n, the singular value decomposition is
-   an m-by-n orthogonal matrix U, an n-by-n diagonal matrix S, and
-   an n-by-n orthogonal matrix V so that A = U*S*V'.
-   <P>
-   The singular values, sigma[k] = S[k][k], are ordered so that
-   sigma[0] >= sigma[1] >= ... >= sigma[n-1].
-   <P>
-   The singular value decompostion always exists, so the constructor will
-   never fail.  The matrix condition number and the effective numerical
-   rank can be computed from this decomposition.
-
-   <p>
-	(Adapted from JAMA, a Java Matrix Library, developed by jointly 
-	by the Mathworks and NIST; see  http://math.nist.gov/javanumerics/jama).
-   */
-template <class Real>
-class SVD 
-{
-
-
-	Array2D<Real> U, V;
-	Array1D<Real> s;
-	int m, n;
-
-  public:
-
-
-   SVD (const Array2D<Real> &Arg) {
-
-
-      m = Arg.dim1();
-      n = Arg.dim2();
-      int nu = std::min(m,n);
-      s = Array1D<Real>(std::min(m+1,n)); 
-      U = Array2D<Real>(m, nu, Real(0));
-      V = Array2D<Real>(n,n);
-      Array1D<Real> e(n);
-      Array1D<Real> work(m);
-	  Array2D<Real> A(Arg.copy());
-      int wantu = 1;  					/* boolean */
-      int wantv = 1;  					/* boolean */
-	  int i=0, j=0, k=0;
-
-      // Reduce A to bidiagonal form, storing the diagonal elements
-      // in s and the super-diagonal elements in e.
-
-      int nct = std::min(m-1,n);
-      int nrt = std::max(0,std::min(n-2,m));
-      for (k = 0; k < std::max(nct,nrt); k++) {
-         if (k < nct) {
-
-            // Compute the transformation for the k-th column and
-            // place the k-th diagonal in s[k].
-            // Compute 2-norm of k-th column without under/overflow.
-            s[k] = 0;
-            for (i = k; i < m; i++) {
-               s[k] = hypot(s[k],A[i][k]);
-            }
-            if (s[k] != 0.0) {
-               if (A[k][k] < 0.0) {
-                  s[k] = -s[k];
-               }
-               for (i = k; i < m; i++) {
-                  A[i][k] /= s[k];
-               }
-               A[k][k] += 1.0;
-            }
-            s[k] = -s[k];
-         }
-         for (j = k+1; j < n; j++) {
-            if ((k < nct) && (s[k] != 0.0))  {
-
-            // Apply the transformation.
-
-               Real t(0.0);
-               for (i = k; i < m; i++) {
-                  t += A[i][k]*A[i][j];
-               }
-               t = -t/A[k][k];
-               for (i = k; i < m; i++) {
-                  A[i][j] += t*A[i][k];
-               }
-            }
-
-            // Place the k-th row of A into e for the
-            // subsequent calculation of the row transformation.
-
-            e[j] = A[k][j];
-         }
-         if (wantu & (k < nct)) {
-
-            // Place the transformation in U for subsequent back
-            // multiplication.
-
-            for (i = k; i < m; i++) {
-               U[i][k] = A[i][k];
-            }
-         }
-         if (k < nrt) {
-
-            // Compute the k-th row transformation and place the
-            // k-th super-diagonal in e[k].
-            // Compute 2-norm without under/overflow.
-            e[k] = 0;
-            for (i = k+1; i < n; i++) {
-               e[k] = hypot(e[k],e[i]);
-            }
-            if (e[k] != 0.0) {
-               if (e[k+1] < 0.0) {
-                  e[k] = -e[k];
-               }
-               for (i = k+1; i < n; i++) {
-                  e[i] /= e[k];
-               }
-               e[k+1] += 1.0;
-            }
-            e[k] = -e[k];
-            if ((k+1 < m) & (e[k] != 0.0)) {
-
-            // Apply the transformation.
-
-               for (i = k+1; i < m; i++) {
-                  work[i] = 0.0;
-               }
-               for (j = k+1; j < n; j++) {
-                  for (i = k+1; i < m; i++) {
-                     work[i] += e[j]*A[i][j];
-                  }
-               }
-               for (j = k+1; j < n; j++) {
-                  Real t(-e[j]/e[k+1]);
-                  for (i = k+1; i < m; i++) {
-                     A[i][j] += t*work[i];
-                  }
-               }
-            }
-            if (wantv) {
-
-            // Place the transformation in V for subsequent
-            // back multiplication.
-
-               for (i = k+1; i < n; i++) {
-                  V[i][k] = e[i];
-               }
-            }
-         }
-      }
-
-      // Set up the final bidiagonal matrix or order p.
-
-      int p = std::min(n,m+1);
-      if (nct < n) {
-         s[nct] = A[nct][nct];
-      }
-      if (m < p) {
-         s[p-1] = 0.0;
-      }
-      if (nrt+1 < p) {
-         e[nrt] = A[nrt][p-1];
-      }
-      e[p-1] = 0.0;
-
-      // If required, generate U.
-
-      if (wantu) {
-         for (j = nct; j < nu; j++) {
-            for (i = 0; i < m; i++) {
-               U[i][j] = 0.0;
-            }
-            U[j][j] = 1.0;
-         }
-         for (k = nct-1; k >= 0; k--) {
-            if (s[k] != 0.0) {
-               for (j = k+1; j < nu; j++) {
-                  Real t(0.0);
-                  for (i = k; i < m; i++) {
-                     t += U[i][k]*U[i][j];
-                  }
-                  t = -t/U[k][k];
-                  for (i = k; i < m; i++) {
-                     U[i][j] += t*U[i][k];
-                  }
-               }
-               for (i = k; i < m; i++ ) {
-                  U[i][k] = -U[i][k];
-               }
-               U[k][k] = 1.0 + U[k][k];
-               for (i = 0; i < k-1; i++) {
-                  U[i][k] = 0.0;
-               }
-            } else {
-               for (i = 0; i < m; i++) {
-                  U[i][k] = 0.0;
-               }
-               U[k][k] = 1.0;
-            }
-         }
-      }
-
-      // If required, generate V.
-
-      if (wantv) {
-         for (k = n-1; k >= 0; k--) {
-            if ((k < nrt) & (e[k] != 0.0)) {
-               for (j = k+1; j < nu; j++) {
-                  Real t(0.0);
-                  for (i = k+1; i < n; i++) {
-                     t += V[i][k]*V[i][j];
-                  }
-                  t = -t/V[k+1][k];
-                  for (i = k+1; i < n; i++) {
-                     V[i][j] += t*V[i][k];
-                  }
-               }
-            }
-            for (i = 0; i < n; i++) {
-               V[i][k] = 0.0;
-            }
-            V[k][k] = 1.0;
-         }
-      }
-
-      // Main iteration loop for the singular values.
-
-      int pp = p-1;
-      int iter = 0;
-      Real eps(pow(2.0,-52.0));
-      while (p > 0) {
-         int k=0;
-		 int kase=0;
-
-         // Here is where a test for too many iterations would go.
-
-         // This section of the program inspects for
-         // negligible elements in the s and e arrays.  On
-         // completion the variables kase and k are set as follows.
-
-         // kase = 1     if s(p) and e[k-1] are negligible and k<p
-         // kase = 2     if s(k) is negligible and k<p
-         // kase = 3     if e[k-1] is negligible, k<p, and
-         //              s(k), ..., s(p) are not negligible (qr step).
-         // kase = 4     if e(p-1) is negligible (convergence).
-
-         for (k = p-2; k >= -1; k--) {
-            if (k == -1) {
-               break;
-            }
-            if (abs(e[k]) <= eps*(abs(s[k]) + abs(s[k+1]))) {
-               e[k] = 0.0;
-               break;
-            }
-         }
-         if (k == p-2) {
-            kase = 4;
-         } else {
-            int ks;
-            for (ks = p-1; ks >= k; ks--) {
-               if (ks == k) {
-                  break;
-               }
-               Real t( (ks != p ? abs(e[ks]) : 0.) + 
-                          (ks != k+1 ? abs(e[ks-1]) : 0.));
-               if (abs(s[ks]) <= eps*t)  {
-                  s[ks] = 0.0;
-                  break;
-               }
-            }
-            if (ks == k) {
-               kase = 3;
-            } else if (ks == p-1) {
-               kase = 1;
-            } else {
-               kase = 2;
-               k = ks;
-            }
-         }
-         k++;
-
-         // Perform the task indicated by kase.
-
-         switch (kase) {
-
-            // Deflate negligible s(p).
-
-            case 1: {
-               Real f(e[p-2]);
-               e[p-2] = 0.0;
-               for (j = p-2; j >= k; j--) {
-                  Real t( hypot(s[j],f));
-                  Real cs(s[j]/t);
-                  Real sn(f/t);
-                  s[j] = t;
-                  if (j != k) {
-                     f = -sn*e[j-1];
-                     e[j-1] = cs*e[j-1];
-                  }
-                  if (wantv) {
-                     for (i = 0; i < n; i++) {
-                        t = cs*V[i][j] + sn*V[i][p-1];
-                        V[i][p-1] = -sn*V[i][j] + cs*V[i][p-1];
-                        V[i][j] = t;
-                     }
-                  }
-               }
-            }
-            break;
-
-            // Split at negligible s(k).
-
-            case 2: {
-               Real f(e[k-1]);
-               e[k-1] = 0.0;
-               for (j = k; j < p; j++) {
-                  Real t(hypot(s[j],f));
-                  Real cs( s[j]/t);
-                  Real sn(f/t);
-                  s[j] = t;
-                  f = -sn*e[j];
-                  e[j] = cs*e[j];
-                  if (wantu) {
-                     for (i = 0; i < m; i++) {
-                        t = cs*U[i][j] + sn*U[i][k-1];
-                        U[i][k-1] = -sn*U[i][j] + cs*U[i][k-1];
-                        U[i][j] = t;
-                     }
-                  }
-               }
-            }
-            break;
-
-            // Perform one qr step.
-
-            case 3: {
-
-               // Calculate the shift.
-   
-               Real scale = std::max(std::max(std::max(std::max(
-                       abs(s[p-1]),abs(s[p-2])),abs(e[p-2])), 
-                       abs(s[k])),abs(e[k]));
-               Real sp = s[p-1]/scale;
-               Real spm1 = s[p-2]/scale;
-               Real epm1 = e[p-2]/scale;
-               Real sk = s[k]/scale;
-               Real ek = e[k]/scale;
-               Real b = ((spm1 + sp)*(spm1 - sp) + epm1*epm1)/2.0;
-               Real c = (sp*epm1)*(sp*epm1);
-               Real shift = 0.0;
-               if ((b != 0.0) || (c != 0.0)) {
-                  shift = sqrt(b*b + c);
-                  if (b < 0.0) {
-                     shift = -shift;
-                  }
-                  shift = c/(b + shift);
-               }
-               Real f = (sk + sp)*(sk - sp) + shift;
-               Real g = sk*ek;
-   
-               // Chase zeros.
-   
-               for (j = k; j < p-1; j++) {
-                  Real t = hypot(f,g);
-                  Real cs = f/t;
-                  Real sn = g/t;
-                  if (j != k) {
-                     e[j-1] = t;
-                  }
-                  f = cs*s[j] + sn*e[j];
-                  e[j] = cs*e[j] - sn*s[j];
-                  g = sn*s[j+1];
-                  s[j+1] = cs*s[j+1];
-                  if (wantv) {
-                     for (i = 0; i < n; i++) {
-                        t = cs*V[i][j] + sn*V[i][j+1];
-                        V[i][j+1] = -sn*V[i][j] + cs*V[i][j+1];
-                        V[i][j] = t;
-                     }
-                  }
-                  t = hypot(f,g);
-                  cs = f/t;
-                  sn = g/t;
-                  s[j] = t;
-                  f = cs*e[j] + sn*s[j+1];
-                  s[j+1] = -sn*e[j] + cs*s[j+1];
-                  g = sn*e[j+1];
-                  e[j+1] = cs*e[j+1];
-                  if (wantu && (j < m-1)) {
-                     for (i = 0; i < m; i++) {
-                        t = cs*U[i][j] + sn*U[i][j+1];
-                        U[i][j+1] = -sn*U[i][j] + cs*U[i][j+1];
-                        U[i][j] = t;
-                     }
-                  }
-               }
-               e[p-2] = f;
-               iter = iter + 1;
-            }
-            break;
-
-            // Convergence.
-
-            case 4: {
-
-               // Make the singular values positive.
-   
-               if (s[k] <= 0.0) {
-                  s[k] = (s[k] < 0.0 ? -s[k] : 0.0);
-                  if (wantv) {
-                     for (i = 0; i <= pp; i++) {
-                        V[i][k] = -V[i][k];
-                     }
-                  }
-               }
-   
-               // Order the singular values.
-   
-               while (k < pp) {
-                  if (s[k] >= s[k+1]) {
-                     break;
-                  }
-                  Real t = s[k];
-                  s[k] = s[k+1];
-                  s[k+1] = t;
-                  if (wantv && (k < n-1)) {
-                     for (i = 0; i < n; i++) {
-                        t = V[i][k+1]; V[i][k+1] = V[i][k]; V[i][k] = t;
-                     }
-                  }
-                  if (wantu && (k < m-1)) {
-                     for (i = 0; i < m; i++) {
-                        t = U[i][k+1]; U[i][k+1] = U[i][k]; U[i][k] = t;
-                     }
-                  }
-                  k++;
-               }
-               iter = 0;
-               p--;
-            }
-            break;
-         }
-      }
-   }
-
-
-   void getU (Array2D<Real> &A) 
-   {
-   	  int minm = std::min(m+1,n);
-
-	  A = Array2D<Real>(m, minm);
-
-	  for (int i=0; i<m; i++)
-	  	for (int j=0; j<minm; j++)
-			A[i][j] = U[i][j];
-   	
-   }
-
-   /* Return the right singular vectors */
-
-   void getV (Array2D<Real> &A) 
-   {
-   	  A = V;
-   }
-
-   /** Return the one-dimensional array of singular values */
-
-   void getSingularValues (Array1D<Real> &x) 
-   {
-      x = s;
-   }
-
-   /** Return the diagonal matrix of singular values
-   @return     S
-   */
-
-   void getS (Array2D<Real> &A) {
-   	  A = Array2D<Real>(n,n);
-      for (int i = 0; i < n; i++) {
-         for (int j = 0; j < n; j++) {
-            A[i][j] = 0.0;
-         }
-         A[i][i] = s[i];
-      }
-   }
-
-   /** Two norm  (max(S)) */
-
-   Real norm2 () {
-      return s[0];
-   }
-
-   /** Two norm of condition number (max(S)/min(S)) */
-
-   Real cond () {
-      return s[0]/s[std::min(m,n)-1];
-   }
-
-   /** Effective numerical matrix rank
-   @return     Number of nonnegligible singular values.
-   */
-
-   int rank () 
-   {
-      Real eps = pow(2.0,-52.0);
-      Real tol = std::max(m,n)*s[0]*eps;
-      int r = 0;
-      for (int i = 0; i < s.dim(); i++) {
-         if (s[i] > tol) {
-            r++;
-         }
-      }
-      return r;
-   }
-};
-
-}
-#endif
-// JAMA_SVD_H
diff --git a/lib/include/tnt/tnt.h b/lib/include/tnt/tnt.h
deleted file mode 100644
index 92463e0..0000000
--- a/lib/include/tnt/tnt.h
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT): Linear Algebra Module
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-#ifndef TNT_H
-#define TNT_H
-
-
-
-//---------------------------------------------------------------------
-// Define this macro if you want  TNT to track some of the out-of-bounds
-// indexing. This can encur a small run-time overhead, but is recommended 
-// while developing code.  It can be turned off for production runs.
-// 
-//       #define TNT_BOUNDS_CHECK
-//---------------------------------------------------------------------
-//
-
-//#define TNT_BOUNDS_CHECK
-
-
-
-#include "tnt_version.h"
-#include "tnt_math_utils.h"
-#include "tnt_array1d.h"
-#include "tnt_array2d.h"
-#include "tnt_array3d.h"
-#include "tnt_array1d_utils.h"
-#include "tnt_array2d_utils.h"
-#include "tnt_array3d_utils.h"
-
-#include "tnt_fortran_array1d.h"
-#include "tnt_fortran_array2d.h"
-#include "tnt_fortran_array3d.h"
-#include "tnt_fortran_array1d_utils.h"
-#include "tnt_fortran_array2d_utils.h"
-#include "tnt_fortran_array3d_utils.h"
-
-#include "tnt_sparse_matrix_csr.h"
-
-#include "tnt_stopwatch.h"
-#include "tnt_subscript.h"
-#include "tnt_vec.h"
-#include "tnt_cmat.h"
-
-
-#endif
-// TNT_H
diff --git a/lib/include/tnt/tnt_array1d.h b/lib/include/tnt/tnt_array1d.h
deleted file mode 100644
index 858df57..0000000
--- a/lib/include/tnt/tnt_array1d.h
+++ /dev/null
@@ -1,278 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_ARRAY1D_H
-#define TNT_ARRAY1D_H
-
-//#include <cstdlib>
-#include <iostream>
-
-#ifdef TNT_BOUNDS_CHECK
-#include <assert.h>
-#endif
-
-
-#include "tnt_i_refvec.h"
-
-namespace TNT
-{
-
-template <class T>
-class Array1D 
-{
-
-  private:
-
-	  /* ... */
-    i_refvec<T> v_;
-    int n_;
-    T* data_;				/* this normally points to v_.begin(), but
-                             * could also point to a portion (subvector)
-							 * of v_.
-                            */
-
-    void copy_(T* p, const T*  q, int len) const;
-    void set_(T* begin,  T* end, const T& val);
- 
-
-  public:
-
-    typedef         T   value_type;
-
-
-	         Array1D();
-	explicit Array1D(int n);
-	         Array1D(int n, const T &a);
-	         Array1D(int n,  T *a);
-    inline   Array1D(const Array1D &A);
-	inline   operator T*();
-	inline   operator const T*();
-	inline   Array1D & operator=(const T &a);
-	inline   Array1D & operator=(const Array1D &A);
-	inline   Array1D & ref(const Array1D &A);
-	         Array1D copy() const;
-		     Array1D & inject(const Array1D & A);
-	inline   T& operator[](int i);
-	inline   const T& operator[](int i) const;
-	inline 	 int dim1() const;
-	inline   int dim() const;
-              ~Array1D();
-
-
-	/* ... extended interface ... */
-
-	inline int ref_count() const;
-	inline Array1D<T> subarray(int i0, int i1);
-
-};
-
-
-
-
-template <class T>
-Array1D<T>::Array1D() : v_(), n_(0), data_(0) {}
-
-template <class T>
-Array1D<T>::Array1D(const Array1D<T> &A) : v_(A.v_),  n_(A.n_), 
-		data_(A.data_)
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Array1D(const Array1D<T> &A) \n";
-#endif
-
-}
-
-
-template <class T>
-Array1D<T>::Array1D(int n) : v_(n), n_(n), data_(v_.begin())
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Array1D(int n) \n";
-#endif
-}
-
-template <class T>
-Array1D<T>::Array1D(int n, const T &val) : v_(n), n_(n), data_(v_.begin()) 
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Array1D(int n, const T& val) \n";
-#endif
-	set_(data_, data_+ n, val);
-
-}
-
-template <class T>
-Array1D<T>::Array1D(int n, T *a) : v_(a), n_(n) , data_(v_.begin())
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Array1D(int n, T* a) \n";
-#endif
-}
-
-template <class T>
-inline Array1D<T>::operator T*()
-{
-	return &(v_[0]);
-}
-
-
-template <class T>
-inline Array1D<T>::operator const T*()
-{
-	return &(v_[0]);
-}
-
-
-
-template <class T>
-inline T& Array1D<T>::operator[](int i) 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i>= 0);
-	assert(i < n_);
-#endif
-	return data_[i]; 
-}
-
-template <class T>
-inline const T& Array1D<T>::operator[](int i) const 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i>= 0);
-	assert(i < n_);
-#endif
-	return data_[i]; 
-}
-
-
-	
-
-template <class T>
-Array1D<T> & Array1D<T>::operator=(const T &a)
-{
-	set_(data_, data_+n_, a);
-	return *this;
-}
-
-template <class T>
-Array1D<T> Array1D<T>::copy() const
-{
-	Array1D A( n_);
-	copy_(A.data_, data_, n_);
-
-	return A;
-}
-
-
-template <class T>
-Array1D<T> & Array1D<T>::inject(const Array1D &A)
-{
-	if (A.n_ == n_)
-		copy_(data_, A.data_, n_);
-
-	return *this;
-}
-
-
-
-
-
-template <class T>
-Array1D<T> & Array1D<T>::ref(const Array1D<T> &A)
-{
-	if (this != &A)
-	{
-		v_ = A.v_;		/* operator= handles the reference counting. */
-		n_ = A.n_;
-		data_ = A.data_; 
-		
-	}
-	return *this;
-}
-
-template <class T>
-Array1D<T> & Array1D<T>::operator=(const Array1D<T> &A)
-{
-	return ref(A);
-}
-
-template <class T>
-inline int Array1D<T>::dim1() const { return n_; }
-
-template <class T>
-inline int Array1D<T>::dim() const { return n_; }
-
-template <class T>
-Array1D<T>::~Array1D() {}
-
-
-/* ............................ exented interface ......................*/
-
-template <class T>
-inline int Array1D<T>::ref_count() const
-{
-	return v_.ref_count();
-}
-
-template <class T>
-inline Array1D<T> Array1D<T>::subarray(int i0, int i1)
-{
-	if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
-	{
-		Array1D<T> X(*this);  /* create a new instance of this array. */
-		X.n_ = i1-i0+1;
-		X.data_ += i0;
-
-		return X;
-	}
-	else
-	{
-		return Array1D<T>();
-	}
-}
-
-
-/* private internal functions */
-
-
-template <class T>
-void Array1D<T>::set_(T* begin, T* end, const T& a)
-{
-	for (T* p=begin; p<end; p++)
-		*p = a;
-
-}
-
-template <class T>
-void Array1D<T>::copy_(T* p, const T* q, int len) const
-{
-	T *end = p + len;
-	while (p<end )
-		*p++ = *q++;
-
-}
-
-
-} /* namespace TNT */
-
-#endif
-/* TNT_ARRAY1D_H */
-
diff --git a/lib/include/tnt/tnt_array1d_utils.h b/lib/include/tnt/tnt_array1d_utils.h
deleted file mode 100644
index 683e0e2..0000000
--- a/lib/include/tnt/tnt_array1d_utils.h
+++ /dev/null
@@ -1,230 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-#ifndef TNT_ARRAY1D_UTILS_H
-#define TNT_ARRAY1D_UTILS_H
-
-#include <cstdlib>
-#include <cassert>
-
-namespace TNT
-{
-
-
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Array1D<T> &A)
-{
-    int N=A.dim1();
-
-#ifdef TNT_DEBUG
-	s << "addr: " << (void *) &A[0] << "\n";
-#endif
-    s << N << "\n";
-    for (int j=0; j<N; j++)
-    {
-       s << A[j] << "\n";
-    }
-    s << "\n";
-
-    return s;
-}
-
-template <class T>
-std::istream& operator>>(std::istream &s, Array1D<T> &A)
-{
-	int N;
-	s >> N;
-
-	Array1D<T> B(N);
-	for (int i=0; i<N; i++)
-		s >> B[i];
-	A = B;
-	return s;
-}
-
-
-
-template <class T>
-Array1D<T> operator+(const Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Array1D<T>();
-
-	else
-	{
-		Array1D<T> C(n);
-
-		for (int i=0; i<n; i++)
-		{
-			C[i] = A[i] + B[i];
-		}
-		return C;
-	}
-}
-
-
-
-template <class T>
-Array1D<T> operator-(const Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Array1D<T>();
-
-	else
-	{
-		Array1D<T> C(n);
-
-		for (int i=0; i<n; i++)
-		{
-			C[i] = A[i] - B[i];
-		}
-		return C;
-	}
-}
-
-
-template <class T>
-Array1D<T> operator*(const Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Array1D<T>();
-
-	else
-	{
-		Array1D<T> C(n);
-
-		for (int i=0; i<n; i++)
-		{
-			C[i] = A[i] * B[i];
-		}
-		return C;
-	}
-}
-
-
-template <class T>
-Array1D<T> operator/(const Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Array1D<T>();
-
-	else
-	{
-		Array1D<T> C(n);
-
-		for (int i=0; i<n; i++)
-		{
-			C[i] = A[i] / B[i];
-		}
-		return C;
-	}
-}
-
-
-
-
-
-
-
-
-
-template <class T>
-Array1D<T>&  operator+=(Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=0; i<n; i++)
-		{
-				A[i] += B[i];
-		}
-	}
-	return A;
-}
-
-
-
-
-template <class T>
-Array1D<T>&  operator-=(Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=0; i<n; i++)
-		{
-				A[i] -= B[i];
-		}
-	}
-	return A;
-}
-
-
-
-template <class T>
-Array1D<T>&  operator*=(Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=0; i<n; i++)
-		{
-				A[i] *= B[i];
-		}
-	}
-	return A;
-}
-
-
-
-
-template <class T>
-Array1D<T>&  operator/=(Array1D<T> &A, const Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=0; i<n; i++)
-		{
-				A[i] /= B[i];
-		}
-	}
-	return A;
-}
-
-
-
-
-
-
-} // namespace TNT
-
-#endif
diff --git a/lib/include/tnt/tnt_array2d.h b/lib/include/tnt/tnt_array2d.h
deleted file mode 100644
index c791575..0000000
--- a/lib/include/tnt/tnt_array2d.h
+++ /dev/null
@@ -1,315 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_ARRAY2D_H
-#define TNT_ARRAY2D_H
-
-#include <cstdlib>
-#include <iostream>
-#ifdef TNT_BOUNDS_CHECK
-#include <assert.h>
-#endif
-
-#include "tnt_array1d.h"
-
-namespace TNT
-{
-
-template <class T>
-class Array2D 
-{
-
-
-  private:
-
-
-
-  	Array1D<T> data_;
-	Array1D<T*> v_;
-	int m_;
-    int n_;
-
-  public:
-
-    typedef         T   value_type;
-	       Array2D();
-	       Array2D(int m, int n);
-	       Array2D(int m, int n,  T *a);
-	       Array2D(int m, int n, const T &a);
-    inline Array2D(const Array2D &A);
-	inline operator T**();
-	inline operator const T**();
-	inline Array2D & operator=(const T &a);
-	inline Array2D & operator=(const Array2D &A);
-	inline Array2D & ref(const Array2D &A);
-	       Array2D copy() const;
-		   Array2D & inject(const Array2D & A);
-	inline T* operator[](int i);
-	inline const T* operator[](int i) const;
-	inline int dim1() const;
-	inline int dim2() const;
-     ~Array2D();
-
-	/* extended interface (not part of the standard) */
-
-
-	inline int ref_count();
-	inline int ref_count_data();
-	inline int ref_count_dim1();
-	Array2D subarray(int i0, int i1, int j0, int j1);
-
-};
-
-
-template <class T>
-Array2D<T>::Array2D() : data_(), v_(), m_(0), n_(0) {} 
-
-template <class T>
-Array2D<T>::Array2D(const Array2D<T> &A) : data_(A.data_), v_(A.v_), 
-	m_(A.m_), n_(A.n_) {}
-
-
-
-
-template <class T>
-Array2D<T>::Array2D(int m, int n) : data_(m*n), v_(m), m_(m), n_(n)
-{
-	if (m>0 && n>0)
-	{
-		T* p = &(data_[0]);
-		for (int i=0; i<m; i++)
-		{
-			v_[i] = p;
-			p += n;
-		}
-	}
-}
-
-
-
-template <class T>
-Array2D<T>::Array2D(int m, int n, const T &val) : data_(m*n), v_(m), 
-													m_(m), n_(n) 
-{
-  if (m>0 && n>0)
-  {
-	data_ = val;
-	T* p  = &(data_[0]);
-	for (int i=0; i<m; i++)
-	{
-			v_[i] = p;
-			p += n;
-	}
-  }
-}
-
-template <class T>
-Array2D<T>::Array2D(int m, int n, T *a) : data_(m*n, a), v_(m), m_(m), n_(n)
-{
-  if (m>0 && n>0)
-  {
-	T* p = &(data_[0]);
-	
-	for (int i=0; i<m; i++)
-	{
-			v_[i] = p;
-			p += n;
-	}
-  }
-}
-
-
-template <class T>
-inline T* Array2D<T>::operator[](int i) 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i >= 0);
-	assert(i < m_);
-#endif
-
-return v_[i]; 
-
-}
-
-
-template <class T>
-inline const T* Array2D<T>::operator[](int i) const
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i >= 0);
-	assert(i < m_);
-#endif
-
-return v_[i]; 
-
-}
-
-template <class T>
-Array2D<T> & Array2D<T>::operator=(const T &a)
-{
-	/* non-optimzied, but will work with subarrays in future verions */
-
-	for (int i=0; i<m_; i++)
-		for (int j=0; j<n_; j++)
-		v_[i][j] = a;
-	return *this;
-}
-
-
-
-
-template <class T>
-Array2D<T> Array2D<T>::copy() const
-{
-	Array2D A(m_, n_);
-
-	for (int i=0; i<m_; i++)
-		for (int j=0; j<n_; j++)
-			A[i][j] = v_[i][j];
-
-
-	return A;
-}
-
-
-template <class T>
-Array2D<T> & Array2D<T>::inject(const Array2D &A)
-{
-	if (A.m_ == m_ &&  A.n_ == n_)
-	{
-		for (int i=0; i<m_; i++)
-			for (int j=0; j<n_; j++)
-				v_[i][j] = A[i][j];
-	}
-	return *this;
-}
-
-
-
-
-template <class T>
-Array2D<T> & Array2D<T>::ref(const Array2D<T> &A)
-{
-	if (this != &A)
-	{
-		v_ = A.v_;
-		data_ = A.data_;
-		m_ = A.m_;
-		n_ = A.n_;
-		
-	}
-	return *this;
-}
-
-
-
-template <class T>
-Array2D<T> & Array2D<T>::operator=(const Array2D<T> &A)
-{
-	return ref(A);
-}
-
-template <class T>
-inline int Array2D<T>::dim1() const { return m_; }
-
-template <class T>
-inline int Array2D<T>::dim2() const { return n_; }
-
-
-template <class T>
-Array2D<T>::~Array2D() {}
-
-
-
-
-template <class T>
-inline Array2D<T>::operator T**()
-{
-	return &(v_[0]);
-}
-template <class T>
-inline Array2D<T>::operator const T**()
-{
-	return &(v_[0]);
-}
-
-/* ............... extended interface ............... */
-/**
-	Create a new view to a subarray defined by the boundaries
-	[i0][i0] and [i1][j1].  The size of the subarray is
-	(i1-i0) by (j1-j0).  If either of these lengths are zero
-	or negative, the subarray view is null.
-
-*/
-template <class T>
-Array2D<T> Array2D<T>::subarray(int i0, int i1, int j0, int j1) 
-{
-	Array2D<T> A;
-	int m = i1-i0+1;
-	int n = j1-j0+1;
-
-	/* if either length is zero or negative, this is an invalide
-		subarray. return a null view.
-	*/
-	if (m<1 || n<1)
-		return A;
-
-	A.data_ = data_;
-	A.m_ = m;
-	A.n_ = n;
-	A.v_ = Array1D<T*>(m);
-	T* p = &(data_[0]) + i0 *  n_ + j0;
-	for (int i=0; i<m; i++)
-	{
-		A.v_[i] = p + i*n_;
-
-	}	
-	return A;
-}
-
-template <class T>
-inline int Array2D<T>::ref_count()
-{
-	return ref_count_data();
-}
-
-
-
-template <class T>
-inline int Array2D<T>::ref_count_data()
-{
-	return data_.ref_count();
-}
-
-template <class T>
-inline int Array2D<T>::ref_count_dim1()
-{
-	return v_.ref_count();
-}
-
-
-
-
-} /* namespace TNT */
-
-#endif
-/* TNT_ARRAY2D_H */
-
diff --git a/lib/include/tnt/tnt_array2d_utils.h b/lib/include/tnt/tnt_array2d_utils.h
deleted file mode 100644
index 7041ed3..0000000
--- a/lib/include/tnt/tnt_array2d_utils.h
+++ /dev/null
@@ -1,287 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-#ifndef TNT_ARRAY2D_UTILS_H
-#define TNT_ARRAY2D_UTILS_H
-
-#include <cstdlib>
-#include <cassert>
-
-namespace TNT
-{
-
-
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Array2D<T> &A)
-{
-    int M=A.dim1();
-    int N=A.dim2();
-
-    s << M << " " << N << "\n";
-
-    for (int i=0; i<M; i++)
-    {
-        for (int j=0; j<N; j++)
-        {
-            s << A[i][j] << " ";
-        }
-        s << "\n";
-    }
-
-
-    return s;
-}
-
-template <class T>
-std::istream& operator>>(std::istream &s, Array2D<T> &A)
-{
-
-    int M, N;
-
-    s >> M >> N;
-
-	Array2D<T> B(M,N);
-
-    for (int i=0; i<M; i++)
-        for (int j=0; j<N; j++)
-        {
-            s >>  B[i][j];
-        }
-
-	A = B;
-    return s;
-}
-
-
-template <class T>
-Array2D<T> operator+(const Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Array2D<T>();
-
-	else
-	{
-		Array2D<T> C(m,n);
-
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				C[i][j] = A[i][j] + B[i][j];
-		}
-		return C;
-	}
-}
-
-template <class T>
-Array2D<T> operator-(const Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Array2D<T>();
-
-	else
-	{
-		Array2D<T> C(m,n);
-
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				C[i][j] = A[i][j] - B[i][j];
-		}
-		return C;
-	}
-}
-
-
-template <class T>
-Array2D<T> operator*(const Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Array2D<T>();
-
-	else
-	{
-		Array2D<T> C(m,n);
-
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				C[i][j] = A[i][j] * B[i][j];
-		}
-		return C;
-	}
-}
-
-
-
-
-template <class T>
-Array2D<T> operator/(const Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Array2D<T>();
-
-	else
-	{
-		Array2D<T> C(m,n);
-
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				C[i][j] = A[i][j] / B[i][j];
-		}
-		return C;
-	}
-}
-
-
-
-
-
-template <class T>
-Array2D<T>&  operator+=(Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				A[i][j] += B[i][j];
-		}
-	}
-	return A;
-}
-
-
-
-template <class T>
-Array2D<T>&  operator-=(Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				A[i][j] -= B[i][j];
-		}
-	}
-	return A;
-}
-
-
-
-template <class T>
-Array2D<T>&  operator*=(Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				A[i][j] *= B[i][j];
-		}
-	}
-	return A;
-}
-
-
-
-
-
-template <class T>
-Array2D<T>&  operator/=(Array2D<T> &A, const Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=0; i<m; i++)
-		{
-			for (int j=0; j<n; j++)
-				A[i][j] /= B[i][j];
-		}
-	}
-	return A;
-}
-
-/**
-    Matrix Multiply:  compute C = A*B, where C[i][j]
-    is the dot-product of row i of A and column j of B.
-
-
-    @param A an (m x n) array
-    @param B an (n x k) array
-    @return the (m x k) array A*B, or a null array (0x0)
-        if the matrices are non-conformant (i.e. the number
-        of columns of A are different than the number of rows of B.)
-
-
-*/
-template <class T>
-Array2D<T> matmult(const Array2D<T> &A, const Array2D<T> &B)
-{
-    if (A.dim2() != B.dim1())
-        return Array2D<T>();
-
-    int M = A.dim1();
-    int N = A.dim2();
-    int K = B.dim2();
-
-    Array2D<T> C(M,K);
-
-    for (int i=0; i<M; i++)
-        for (int j=0; j<K; j++)
-        {
-            T sum = 0;
-
-            for (int k=0; k<N; k++)
-                sum += A[i][k] * B [k][j];
-
-            C[i][j] = sum;
-        }
-
-    return C;
-
-}
-
-} // namespace TNT
-
-#endif
diff --git a/lib/include/tnt/tnt_array3d.h b/lib/include/tnt/tnt_array3d.h
deleted file mode 100644
index c210d2e..0000000
--- a/lib/include/tnt/tnt_array3d.h
+++ /dev/null
@@ -1,296 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_ARRAY3D_H
-#define TNT_ARRAY3D_H
-
-#include <cstdlib>
-#include <iostream>
-#ifdef TNT_BOUNDS_CHECK
-#include <assert.h>
-#endif
-
-#include "tnt_array1d.h"
-#include "tnt_array2d.h"
-
-namespace TNT
-{
-
-template <class T>
-class Array3D 
-{
-
-
-  private:
-  	Array1D<T> data_;
-	Array2D<T*> v_;
-	int m_;
-    int n_;
-	int g_;
-
-
-  public:
-
-    typedef         T   value_type;
-
-	       Array3D();
-	       Array3D(int m, int n, int g);
-	       Array3D(int m, int n, int g,  T val);
-	       Array3D(int m, int n, int g, T *a);
-
-	inline operator T***();
-	inline operator const T***();
-    inline Array3D(const Array3D &A);
-	inline Array3D & operator=(const T &a);
-	inline Array3D & operator=(const Array3D &A);
-	inline Array3D & ref(const Array3D &A);
-	       Array3D copy() const;
-		   Array3D & inject(const Array3D & A);
-
-	inline T** operator[](int i);
-	inline const T* const * operator[](int i) const;
-	inline int dim1() const;
-	inline int dim2() const;
-	inline int dim3() const;
-               ~Array3D();
-
-	/* extended interface */
-
-	inline int ref_count(){ return data_.ref_count(); }
-   Array3D subarray(int i0, int i1, int j0, int j1, 
-		   		int k0, int k1);
-};
-
-template <class T>
-Array3D<T>::Array3D() : data_(), v_(), m_(0), n_(0) {}
-
-template <class T>
-Array3D<T>::Array3D(const Array3D<T> &A) : data_(A.data_), 
-	v_(A.v_), m_(A.m_), n_(A.n_), g_(A.g_)
-{
-}
-
-
-
-template <class T>
-Array3D<T>::Array3D(int m, int n, int g) : data_(m*n*g), v_(m,n),
-	m_(m), n_(n), g_(g)
-{
-
-  if (m>0 && n>0 && g>0)
-  {
-	T* p = & (data_[0]);
-	int ng = n_*g_;
-
-	for (int i=0; i<m_; i++)
-	{	
-		T* ping = p+ i*ng;
-		for (int j=0; j<n; j++)
-			v_[i][j] = ping + j*g_;
-	}
-  }
-}
-
-
-
-template <class T>
-Array3D<T>::Array3D(int m, int n, int g, T val) : data_(m*n*g, val), 
-	v_(m,n), m_(m), n_(n), g_(g)
-{
-  if (m>0 && n>0 && g>0)
-  {
-
-	T* p = & (data_[0]);
-	int ng = n_*g_;
-
-	for (int i=0; i<m_; i++)
-	{	
-		T* ping = p+ i*ng;
-		for (int j=0; j<n; j++)
-			v_[i][j] = ping + j*g_;
-	}
-  }
-}
-
-
-
-template <class T>
-Array3D<T>::Array3D(int m, int n, int g, T* a) : 
-		data_(m*n*g, a), v_(m,n), m_(m), n_(n), g_(g)
-{
-
-  if (m>0 && n>0 && g>0)
-  {
-	T* p = & (data_[0]);
-	int ng = n_*g_;
-
-	for (int i=0; i<m_; i++)
-	{	
-		T* ping = p+ i*ng;
-		for (int j=0; j<n; j++)
-			v_[i][j] = ping + j*g_;
-	}
-  }
-}
-
-
-
-template <class T>
-inline T** Array3D<T>::operator[](int i) 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i >= 0);
-	assert(i < m_);
-#endif
-
-return v_[i]; 
-
-}
-
-template <class T>
-inline const T* const * Array3D<T>::operator[](int i) const 
-{ return v_[i]; }
-
-template <class T>
-Array3D<T> & Array3D<T>::operator=(const T &a)
-{
-	for (int i=0; i<m_; i++)
-		for (int j=0; j<n_; j++)
-			for (int k=0; k<g_; k++)
-				v_[i][j][k] = a;
-
-	return *this;
-}
-
-template <class T>
-Array3D<T> Array3D<T>::copy() const
-{
-	Array3D A(m_, n_, g_);
-	for (int i=0; i<m_; i++)
-		for (int j=0; j<n_; j++)
-			for (int k=0; k<g_; k++)
-				A.v_[i][j][k] = v_[i][j][k];
-
-	return A;
-}
-
-
-template <class T>
-Array3D<T> & Array3D<T>::inject(const Array3D &A)
-{
-	if (A.m_ == m_ &&  A.n_ == n_ && A.g_ == g_)
-
-	for (int i=0; i<m_; i++)
-		for (int j=0; j<n_; j++)
-			for (int k=0; k<g_; k++)
-				v_[i][j][k] = A.v_[i][j][k];
-
-	return *this;
-}
-
-
-
-template <class T>
-Array3D<T> & Array3D<T>::ref(const Array3D<T> &A)
-{
-	if (this != &A)
-	{
-		m_ = A.m_;
-		n_ = A.n_;
-		g_ = A.g_;
-		v_ = A.v_;
-		data_ = A.data_;
-	}
-	return *this;
-}
-
-template <class T>
-Array3D<T> & Array3D<T>::operator=(const Array3D<T> &A)
-{
-	return ref(A);
-}
-
-
-template <class T>
-inline int Array3D<T>::dim1() const { return m_; }
-
-template <class T>
-inline int Array3D<T>::dim2() const { return n_; }
-
-template <class T>
-inline int Array3D<T>::dim3() const { return g_; }
-
-
-
-template <class T>
-Array3D<T>::~Array3D() {}
-
-template <class T>
-inline Array3D<T>::operator T***()
-{
-	return v_;
-}
-
-
-template <class T>
-inline Array3D<T>::operator const T***()
-{
-	return v_;
-}
-
-/* extended interface */
-template <class T>
-Array3D<T> Array3D<T>::subarray(int i0, int i1, int j0,
-	int j1, int k0, int k1)
-{
-
-	/* check that ranges are valid. */
-	if (!( 0 <= i0 && i0 <= i1 && i1 < m_ &&
-	      0 <= j0 && j0 <= j1 && j1 < n_ &&
-	      0 <= k0 && k0 <= k1 && k1 < g_))
-		return Array3D<T>();  /* null array */
-
-
-	Array3D<T> A;
-	A.data_ = data_;
-	A.m_ = i1-i0+1;
-	A.n_ = j1-j0+1;
-	A.g_ = k1-k0+1;
-	A.v_ = Array2D<T*>(A.m_,A.n_);
-	T* p = &(data_[0]) + i0*n_*g_ + j0*g_ + k0; 
-
-	for (int i=0; i<A.m_; i++)
-	{
-		T* ping = p + i*n_*g_;
-		for (int j=0; j<A.n_; j++)
-			A.v_[i][j] = ping + j*g_ ;
-	}
-
-	return A;
-}
-	
-
-
-} /* namespace TNT */
-
-#endif
-/* TNT_ARRAY3D_H */
-
diff --git a/lib/include/tnt/tnt_array3d_utils.h b/lib/include/tnt/tnt_array3d_utils.h
deleted file mode 100644
index 5acdc1d..0000000
--- a/lib/include/tnt/tnt_array3d_utils.h
+++ /dev/null
@@ -1,236 +0,0 @@
-
-
-#ifndef TNT_ARRAY3D_UTILS_H
-#define TNT_ARRAY3D_UTILS_H
-
-#include <cstdlib>
-#include <cassert>
-
-namespace TNT
-{
-
-
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Array3D<T> &A)
-{
-    int M=A.dim1();
-    int N=A.dim2();
-    int K=A.dim3();
-
-    s << M << " " << N << " " << K << "\n";
-
-    for (int i=0; i<M; i++)
-    {
-        for (int j=0; j<N; j++)
-        {
-			for (int k=0; k<K; k++)
-            	s << A[i][j][k] << " ";
-			s << "\n";
-        }
-        s << "\n";
-    }
-
-
-    return s;
-}
-
-template <class T>
-std::istream& operator>>(std::istream &s, Array3D<T> &A)
-{
-
-    int M, N, K;
-
-    s >> M >> N >> K;
-
-	Array3D<T> B(M,N,K);
-
-    for (int i=0; i<M; i++)
-        for (int j=0; j<N; j++)
-			for (int k=0; k<K; k++)
-            	s >>  B[i][j][k];
-
-	A = B;
-    return s;
-}
-
-
-
-template <class T>
-Array3D<T> operator+(const Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Array3D<T>();
-
-	else
-	{
-		Array3D<T> C(m,n,p);
-
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-				C[i][j][k] = A[i][j][k] + B[i][j][k];
-
-		return C;
-	}
-}
-
-
-template <class T>
-Array3D<T> operator-(const Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Array3D<T>();
-
-	else
-	{
-		Array3D<T> C(m,n,p);
-
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-				C[i][j][k] = A[i][j][k] - B[i][j][k];
-
-		return C;
-	}
-}
-
-
-
-
-template <class T>
-Array3D<T> operator*(const Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Array3D<T>();
-
-	else
-	{
-		Array3D<T> C(m,n,p);
-
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-				C[i][j][k] = A[i][j][k] * B[i][j][k];
-
-		return C;
-	}
-}
-
-
-template <class T>
-Array3D<T> operator/(const Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Array3D<T>();
-
-	else
-	{
-		Array3D<T> C(m,n,p);
-
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-				C[i][j][k] = A[i][j][k] / B[i][j][k];
-
-		return C;
-	}
-}
-
-
-
-template <class T>
-Array3D<T>& operator+=(Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-					A[i][j][k] += B[i][j][k];
-	}
-
-	return A;
-}
-
-template <class T>
-Array3D<T>& operator-=(Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-					A[i][j][k] -= B[i][j][k];
-	}
-
-	return A;
-}
-
-template <class T>
-Array3D<T>& operator*=(Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-					A[i][j][k] *= B[i][j][k];
-	}
-
-	return A;
-}
-
-
-template <class T>
-Array3D<T>& operator/=(Array3D<T> &A, const Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=0; i<m; i++)
-			for (int j=0; j<n; j++)
-				for (int k=0; k<p; k++)
-					A[i][j][k] /= B[i][j][k];
-	}
-
-	return A;
-}
-
-
-
-
-
-} // namespace TNT
-
-#endif
diff --git a/lib/include/tnt/tnt_cmat.h b/lib/include/tnt/tnt_cmat.h
deleted file mode 100644
index 5ff4c48..0000000
--- a/lib/include/tnt/tnt_cmat.h
+++ /dev/null
@@ -1,580 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-// C compatible matrix: row-oriented, 0-based [i][j] and 1-based (i,j) indexing
-//
-
-#ifndef TNT_CMAT_H
-#define TNT_CMAT_H
-
-#include "tnt_subscript.h"
-#include "tnt_vec.h"
-#include <cstdlib>
-#include <cassert>
-#include <iostream>
-#include <sstream>
-
-namespace TNT
-{
-
-
-template <class T>
-class Matrix 
-{
-
-
-  public:
-
-    typedef Subscript   size_type;
-    typedef         T   value_type;
-    typedef         T   element_type;
-    typedef         T*  pointer;
-    typedef         T*  iterator;
-    typedef         T&  reference;
-    typedef const   T*  const_iterator;
-    typedef const   T&  const_reference;
-
-    Subscript lbound() const { return 1;}
- 
-  protected:
-    Subscript m_;
-    Subscript n_;
-    Subscript mn_;      // total size
-    T* v_;                  
-    T** row_;           
-    T* vm1_ ;       // these point to the same data, but are 1-based 
-    T** rowm1_;
-
-    // internal helper function to create the array
-    // of row pointers
-
-    void initialize(Subscript M, Subscript N)
-    {
-        mn_ = M*N;
-        m_ = M;
-        n_ = N;
-
-        v_ = new T[mn_]; 
-        row_ = new T*[M];
-        rowm1_ = new T*[M];
-
-        assert(v_  != NULL);
-        assert(row_  != NULL);
-        assert(rowm1_ != NULL);
-
-        T* p = v_;              
-        vm1_ = v_ - 1;
-        for (Subscript i=0; i<M; i++)
-        {
-            row_[i] = p;
-            rowm1_[i] = p-1;
-            p += N ;
-            
-        }
-
-        rowm1_ -- ;     // compensate for 1-based offset
-    }
-   
-    void copy(const T*  v)
-    {
-        Subscript N = m_ * n_;
-        Subscript i;
-
-#ifdef TNT_UNROLL_LOOPS
-        Subscript Nmod4 = N & 3;
-        Subscript N4 = N - Nmod4;
-
-        for (i=0; i<N4; i+=4)
-        {
-            v_[i] = v[i];
-            v_[i+1] = v[i+1];
-            v_[i+2] = v[i+2];
-            v_[i+3] = v[i+3];
-        }
-
-        for (i=N4; i< N; i++)
-            v_[i] = v[i];
-#else
-
-        for (i=0; i< N; i++)
-            v_[i] = v[i];
-#endif      
-    }
-
-    void set(const T& val)
-    {
-        Subscript N = m_ * n_;
-        Subscript i;
-
-#ifdef TNT_UNROLL_LOOPS
-        Subscript Nmod4 = N & 3;
-        Subscript N4 = N - Nmod4;
-
-        for (i=0; i<N4; i+=4)
-        {
-            v_[i] = val;
-            v_[i+1] = val;
-            v_[i+2] = val;
-            v_[i+3] = val; 
-        }
-
-        for (i=N4; i< N; i++)
-            v_[i] = val;
-#else
-
-        for (i=0; i< N; i++)
-            v_[i] = val;
-        
-#endif      
-    }
-    
-
-    
-    void destroy()
-    {     
-        /* do nothing, if no memory has been previously allocated */
-        if (v_ == NULL) return ;
-
-        /* if we are here, then matrix was previously allocated */
-        if (v_ != NULL) delete [] (v_);     
-        if (row_ != NULL) delete [] (row_);
-
-        /* return rowm1_ back to original value */
-        rowm1_ ++;
-        if (rowm1_ != NULL ) delete [] (rowm1_);
-    }
-
-
-  public:
-
-    operator T**(){ return  row_; }
-    operator T**() const { return row_; }
-
-
-    Subscript size() const { return mn_; }
-
-    // constructors
-
-    Matrix() : m_(0), n_(0), mn_(0), v_(0), row_(0), vm1_(0), rowm1_(0) {};
-
-    Matrix(const Matrix<T> &A)
-    {
-        initialize(A.m_, A.n_);
-        copy(A.v_);
-    }
-
-    Matrix(Subscript M, Subscript N, const T& value = T())
-    {
-        initialize(M,N);
-        set(value);
-    }
-
-    Matrix(Subscript M, Subscript N, const T* v)
-    {
-        initialize(M,N);
-        copy(v);
-    }
-
-    Matrix(Subscript M, Subscript N, const char *s)
-    {
-        initialize(M,N);
-        //std::istrstream ins(s);
-        std::istringstream ins(s);
-
-        Subscript i, j;
-
-        for (i=0; i<M; i++)
-            for (j=0; j<N; j++)
-                ins >> row_[i][j];
-    }
-
-    // destructor
-    //
-    ~Matrix()
-    {
-        destroy();
-    }
-
-
-    // reallocating
-    //
-    Matrix<T>& newsize(Subscript M, Subscript N)
-    {
-        if (num_rows() == M && num_cols() == N)
-            return *this;
-
-        destroy();
-        initialize(M,N);
-        
-        return *this;
-    }
-
-
-
-
-    // assignments
-    //
-    Matrix<T>& operator=(const Matrix<T> &A)
-    {
-        if (v_ == A.v_)
-            return *this;
-
-        if (m_ == A.m_  && n_ == A.n_)      // no need to re-alloc
-            copy(A.v_);
-
-        else
-        {
-            destroy();
-            initialize(A.m_, A.n_);
-            copy(A.v_);
-        }
-
-        return *this;
-    }
-        
-    Matrix<T>& operator=(const T& scalar)
-    { 
-        set(scalar); 
-        return *this;
-    }
-
-
-    Subscript dim(Subscript d) const 
-    {
-#ifdef TNT_BOUNDS_CHECK
-        assert( d >= 1);
-        assert( d <= 2);
-#endif
-        return (d==1) ? m_ : ((d==2) ? n_ : 0); 
-    }
-
-    Subscript num_rows() const { return m_; }
-    Subscript num_cols() const { return n_; }
-
-
-
-
-    inline T* operator[](Subscript i)
-    {
-#ifdef TNT_BOUNDS_CHECK
-        assert(0<=i);
-        assert(i < m_) ;
-#endif
-        return row_[i];
-    }
-
-    inline const T* operator[](Subscript i) const
-    {
-#ifdef TNT_BOUNDS_CHECK
-        assert(0<=i);
-        assert(i < m_) ;
-#endif
-        return row_[i];
-    }
-
-    inline reference operator()(Subscript i)
-    { 
-#ifdef TNT_BOUNDS_CHECK
-        assert(1<=i);
-        assert(i <= mn_) ;
-#endif
-        return vm1_[i]; 
-    }
-
-    inline const_reference operator()(Subscript i) const
-    { 
-#ifdef TNT_BOUNDS_CHECK
-        assert(1<=i);
-        assert(i <= mn_) ;
-#endif
-        return vm1_[i]; 
-    }
-
-
-
-    inline reference operator()(Subscript i, Subscript j)
-    { 
-#ifdef TNT_BOUNDS_CHECK
-        assert(1<=i);
-        assert(i <= m_) ;
-        assert(1<=j);
-        assert(j <= n_);
-#endif
-        return  rowm1_[i][j]; 
-    }
-
-
-    
-    inline const_reference operator() (Subscript i, Subscript j) const
-    {
-#ifdef TNT_BOUNDS_CHECK
-        assert(1<=i);
-        assert(i <= m_) ;
-        assert(1<=j);
-        assert(j <= n_);
-#endif
-        return rowm1_[i][j]; 
-    }
-
-
-
-
-};
-
-
-/* ***************************  I/O  ********************************/
-
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Matrix<T> &A)
-{
-    Subscript M=A.num_rows();
-    Subscript N=A.num_cols();
-
-    s << M << " " << N << "\n";
-
-    for (Subscript i=0; i<M; i++)
-    {
-        for (Subscript j=0; j<N; j++)
-        {
-            s << A[i][j] << " ";
-        }
-        s << "\n";
-    }
-
-
-    return s;
-}
-
-template <class T>
-std::istream& operator>>(std::istream &s, Matrix<T> &A)
-{
-
-    Subscript M, N;
-
-    s >> M >> N;
-
-    if ( !(M == A.num_rows() && N == A.num_cols() ))
-    {
-        A.newsize(M,N);
-    }
-
-
-    for (Subscript i=0; i<M; i++)
-        for (Subscript j=0; j<N; j++)
-        {
-            s >>  A[i][j];
-        }
-
-
-    return s;
-}
-
-// *******************[ basic matrix algorithms ]***************************
-
-
-template <class T>
-Matrix<T> operator+(const Matrix<T> &A, 
-    const Matrix<T> &B)
-{
-    Subscript M = A.num_rows();
-    Subscript N = A.num_cols();
-
-    assert(M==B.num_rows());
-    assert(N==B.num_cols());
-
-    Matrix<T> tmp(M,N);
-    Subscript i,j;
-
-    for (i=0; i<M; i++)
-        for (j=0; j<N; j++)
-            tmp[i][j] = A[i][j] + B[i][j];
-
-    return tmp;
-}
-
-template <class T>
-Matrix<T> operator-(const Matrix<T> &A, 
-    const Matrix<T> &B)
-{
-    Subscript M = A.num_rows();
-    Subscript N = A.num_cols();
-
-    assert(M==B.num_rows());
-    assert(N==B.num_cols());
-
-    Matrix<T> tmp(M,N);
-    Subscript i,j;
-
-    for (i=0; i<M; i++)
-        for (j=0; j<N; j++)
-            tmp[i][j] = A[i][j] - B[i][j];
-
-    return tmp;
-}
-
-template <class T>
-Matrix<T> mult_element(const Matrix<T> &A, 
-    const Matrix<T> &B)
-{
-    Subscript M = A.num_rows();
-    Subscript N = A.num_cols();
-
-    assert(M==B.num_rows());
-    assert(N==B.num_cols());
-
-    Matrix<T> tmp(M,N);
-    Subscript i,j;
-
-    for (i=0; i<M; i++)
-        for (j=0; j<N; j++)
-            tmp[i][j] = A[i][j] * B[i][j];
-
-    return tmp;
-}
-
-
-template <class T>
-Matrix<T> transpose(const Matrix<T> &A)
-{
-    Subscript M = A.num_rows();
-    Subscript N = A.num_cols();
-
-    Matrix<T> S(N,M);
-    Subscript i, j;
-
-    for (i=0; i<M; i++)
-        for (j=0; j<N; j++)
-            S[j][i] = A[i][j];
-
-    return S;
-}
-
-
-    
-template <class T>
-inline Matrix<T> matmult(const Matrix<T>  &A, 
-    const Matrix<T> &B)
-{
-
-#ifdef TNT_BOUNDS_CHECK
-    assert(A.num_cols() == B.num_rows());
-#endif
-
-    Subscript M = A.num_rows();
-    Subscript N = A.num_cols();
-    Subscript K = B.num_cols();
-
-    Matrix<T> tmp(M,K);
-    T sum;
-
-    for (Subscript i=0; i<M; i++)
-    for (Subscript k=0; k<K; k++)
-    {
-        sum = 0;
-        for (Subscript j=0; j<N; j++)
-            sum = sum +  A[i][j] * B[j][k];
-
-        tmp[i][k] = sum; 
-    }
-
-    return tmp;
-}
-
-template <class T>
-inline Matrix<T> operator*(const Matrix<T>  &A, 
-    const Matrix<T> &B)
-{
-    return matmult(A,B);
-}
-
-template <class T>
-inline int matmult(Matrix<T>& C, const Matrix<T>  &A, 
-    const Matrix<T> &B)
-{
-
-    assert(A.num_cols() == B.num_rows());
-
-    Subscript M = A.num_rows();
-    Subscript N = A.num_cols();
-    Subscript K = B.num_cols();
-
-    C.newsize(M,K);
-
-    T sum;
-
-    const T* row_i;
-    const T* col_k;
-
-    for (Subscript i=0; i<M; i++)
-    for (Subscript k=0; k<K; k++)
-    {
-        row_i  = &(A[i][0]);
-        col_k  = &(B[0][k]);
-        sum = 0;
-        for (Subscript j=0; j<N; j++)
-        {
-            sum  += *row_i * *col_k;
-            row_i++;
-            col_k += K;
-        }
-        C[i][k] = sum; 
-    }
-
-    return 0;
-}
-
-
-template <class T>
-Vector<T> matmult(const Matrix<T>  &A, const Vector<T> &x)
-{
-
-#ifdef TNT_BOUNDS_CHECK
-    assert(A.num_cols() == x.dim());
-#endif
-
-    Subscript M = A.num_rows();
-    Subscript N = A.num_cols();
-
-    Vector<T> tmp(M);
-    T sum;
-
-    for (Subscript i=0; i<M; i++)
-    {
-        sum = 0;
-        const T* rowi = A[i];
-        for (Subscript j=0; j<N; j++)
-            sum = sum +  rowi[j] * x[j];
-
-        tmp[i] = sum; 
-    }
-
-    return tmp;
-}
-
-template <class T>
-inline Vector<T> operator*(const Matrix<T>  &A, const Vector<T> &x)
-{
-    return matmult(A,x);
-}
-
-} // namespace TNT
-
-#endif
-// CMAT_H
diff --git a/lib/include/tnt/tnt_fortran_array1d.h b/lib/include/tnt/tnt_fortran_array1d.h
deleted file mode 100644
index ad3bba0..0000000
--- a/lib/include/tnt/tnt_fortran_array1d.h
+++ /dev/null
@@ -1,267 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_FORTRAN_ARRAY1D_H
-#define TNT_FORTRAN_ARRAY1D_H
-
-#include <cstdlib>
-#include <iostream>
-
-#ifdef TNT_BOUNDS_CHECK
-#include <assert.h>
-#endif
-
-
-#include "tnt_i_refvec.h"
-
-namespace TNT
-{
-
-template <class T>
-class Fortran_Array1D 
-{
-
-  private:
-
-    i_refvec<T> v_;
-    int n_;
-    T* data_;				/* this normally points to v_.begin(), but
-                             * could also point to a portion (subvector)
-							 * of v_.
-                            */
-
-    void initialize_(int n);
-    void copy_(T* p, const T*  q, int len) const;
-    void set_(T* begin,  T* end, const T& val);
- 
-
-  public:
-
-    typedef         T   value_type;
-
-
-	         Fortran_Array1D();
-	explicit Fortran_Array1D(int n);
-	         Fortran_Array1D(int n, const T &a);
-	         Fortran_Array1D(int n,  T *a);
-    inline   Fortran_Array1D(const Fortran_Array1D &A);
-	inline   Fortran_Array1D & operator=(const T &a);
-	inline   Fortran_Array1D & operator=(const Fortran_Array1D &A);
-	inline   Fortran_Array1D & ref(const Fortran_Array1D &A);
-	         Fortran_Array1D copy() const;
-		     Fortran_Array1D & inject(const Fortran_Array1D & A);
-	inline   T& operator()(int i);
-	inline   const T& operator()(int i) const;
-	inline 	 int dim1() const;
-	inline   int dim() const;
-              ~Fortran_Array1D();
-
-
-	/* ... extended interface ... */
-
-	inline int ref_count() const;
-	inline Fortran_Array1D<T> subarray(int i0, int i1);
-
-};
-
-
-
-
-template <class T>
-Fortran_Array1D<T>::Fortran_Array1D() : v_(), n_(0), data_(0) {}
-
-template <class T>
-Fortran_Array1D<T>::Fortran_Array1D(const Fortran_Array1D<T> &A) : v_(A.v_),  n_(A.n_), 
-		data_(A.data_)
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Fortran_Array1D(const Fortran_Array1D<T> &A) \n";
-#endif
-
-}
-
-
-template <class T>
-Fortran_Array1D<T>::Fortran_Array1D(int n) : v_(n), n_(n), data_(v_.begin())
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Fortran_Array1D(int n) \n";
-#endif
-}
-
-template <class T>
-Fortran_Array1D<T>::Fortran_Array1D(int n, const T &val) : v_(n), n_(n), data_(v_.begin()) 
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Fortran_Array1D(int n, const T& val) \n";
-#endif
-	set_(data_, data_+ n, val);
-
-}
-
-template <class T>
-Fortran_Array1D<T>::Fortran_Array1D(int n, T *a) : v_(a), n_(n) , data_(v_.begin())
-{
-#ifdef TNT_DEBUG
-	std::cout << "Created Fortran_Array1D(int n, T* a) \n";
-#endif
-}
-
-template <class T>
-inline T& Fortran_Array1D<T>::operator()(int i) 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i>= 1);
-	assert(i <= n_);
-#endif
-	return data_[i-1]; 
-}
-
-template <class T>
-inline const T& Fortran_Array1D<T>::operator()(int i) const 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i>= 1);
-	assert(i <= n_);
-#endif
-	return data_[i-1]; 
-}
-
-
-	
-
-template <class T>
-Fortran_Array1D<T> & Fortran_Array1D<T>::operator=(const T &a)
-{
-	set_(data_, data_+n_, a);
-	return *this;
-}
-
-template <class T>
-Fortran_Array1D<T> Fortran_Array1D<T>::copy() const
-{
-	Fortran_Array1D A( n_);
-	copy_(A.data_, data_, n_);
-
-	return A;
-}
-
-
-template <class T>
-Fortran_Array1D<T> & Fortran_Array1D<T>::inject(const Fortran_Array1D &A)
-{
-	if (A.n_ == n_)
-		copy_(data_, A.data_, n_);
-
-	return *this;
-}
-
-
-
-
-
-template <class T>
-Fortran_Array1D<T> & Fortran_Array1D<T>::ref(const Fortran_Array1D<T> &A)
-{
-	if (this != &A)
-	{
-		v_ = A.v_;		/* operator= handles the reference counting. */
-		n_ = A.n_;
-		data_ = A.data_; 
-		
-	}
-	return *this;
-}
-
-template <class T>
-Fortran_Array1D<T> & Fortran_Array1D<T>::operator=(const Fortran_Array1D<T> &A)
-{
-	return ref(A);
-}
-
-template <class T>
-inline int Fortran_Array1D<T>::dim1() const { return n_; }
-
-template <class T>
-inline int Fortran_Array1D<T>::dim() const { return n_; }
-
-template <class T>
-Fortran_Array1D<T>::~Fortran_Array1D() {}
-
-
-/* ............................ exented interface ......................*/
-
-template <class T>
-inline int Fortran_Array1D<T>::ref_count() const
-{
-	return v_.ref_count();
-}
-
-template <class T>
-inline Fortran_Array1D<T> Fortran_Array1D<T>::subarray(int i0, int i1)
-{
-#ifdef TNT_DEBUG
-		std::cout << "entered subarray. \n";
-#endif
-	if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
-	{
-		Fortran_Array1D<T> X(*this);  /* create a new instance of this array. */
-		X.n_ = i1-i0+1;
-		X.data_ += i0;
-
-		return X;
-	}
-	else
-	{
-#ifdef TNT_DEBUG
-		std::cout << "subarray:  null return.\n";
-#endif
-		return Fortran_Array1D<T>();
-	}
-}
-
-
-/* private internal functions */
-
-
-template <class T>
-void Fortran_Array1D<T>::set_(T* begin, T* end, const T& a)
-{
-	for (T* p=begin; p<end; p++)
-		*p = a;
-
-}
-
-template <class T>
-void Fortran_Array1D<T>::copy_(T* p, const T* q, int len) const
-{
-	T *end = p + len;
-	while (p<end )
-		*p++ = *q++;
-
-}
-
-
-} /* namespace TNT */
-
-#endif
-/* TNT_FORTRAN_ARRAY1D_H */
-
diff --git a/lib/include/tnt/tnt_fortran_array1d_utils.h b/lib/include/tnt/tnt_fortran_array1d_utils.h
deleted file mode 100644
index b037b17..0000000
--- a/lib/include/tnt/tnt_fortran_array1d_utils.h
+++ /dev/null
@@ -1,242 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-#ifndef TNT_FORTRAN_ARRAY1D_UTILS_H
-#define TNT_FORTRAN_ARRAY1D_UTILS_H
-
-#include <iostream>
-
-namespace TNT
-{
-
-
-/**
-	Write an array to a character outstream.  Output format is one that can
-	be read back in via the in-stream operator: one integer
-	denoting the array dimension (n), followed by n elements,
-	one per line.  
-
-*/
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Fortran_Array1D<T> &A)
-{
-    int N=A.dim1();
-
-    s << N << "\n";
-    for (int j=1; j<=N; j++)
-    {
-       s << A(j) << "\n";
-    }
-    s << "\n";
-
-    return s;
-}
-
-/**
-	Read an array from a character stream.  Input format
-	is one integer, denoting the dimension (n), followed
-	by n whitespace-separated elments.  Newlines are ignored
-
-	<p>
-	Note: the array being read into references new memory
-	storage. If the intent is to fill an existing conformant
-	array, use <code> cin >> B;  A.inject(B) ); </code>
-	instead or read the elements in one-a-time by hand.
-
-	@param s the charater to read from (typically <code>std::in</code>)
-	@param A the array to read into.
-*/
-template <class T>
-std::istream& operator>>(std::istream &s, Fortran_Array1D<T> &A)
-{
-	int N;
-	s >> N;
-
-	Fortran_Array1D<T> B(N);
-	for (int i=1; i<=N; i++)
-		s >> B(i);
-	A = B;
-	return s;
-}
-
-
-template <class T>
-Fortran_Array1D<T> operator+(const Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Fortran_Array1D<T>();
-
-	else
-	{
-		Fortran_Array1D<T> C(n);
-
-		for (int i=1; i<=n; i++)
-		{
-			C(i) = A(i) + B(i);
-		}
-		return C;
-	}
-}
-
-
-
-template <class T>
-Fortran_Array1D<T> operator-(const Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Fortran_Array1D<T>();
-
-	else
-	{
-		Fortran_Array1D<T> C(n);
-
-		for (int i=1; i<=n; i++)
-		{
-			C(i) = A(i) - B(i);
-		}
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array1D<T> operator*(const Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Fortran_Array1D<T>();
-
-	else
-	{
-		Fortran_Array1D<T> C(n);
-
-		for (int i=1; i<=n; i++)
-		{
-			C(i) = A(i) * B(i);
-		}
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array1D<T> operator/(const Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() != n )
-		return Fortran_Array1D<T>();
-
-	else
-	{
-		Fortran_Array1D<T> C(n);
-
-		for (int i=1; i<=n; i++)
-		{
-			C(i) = A(i) / B(i);
-		}
-		return C;
-	}
-}
-
-
-
-
-
-
-
-
-
-template <class T>
-Fortran_Array1D<T>&  operator+=(Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=1; i<=n; i++)
-		{
-				A(i) += B(i);
-		}
-	}
-	return A;
-}
-
-
-
-
-template <class T>
-Fortran_Array1D<T>&  operator-=(Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=1; i<=n; i++)
-		{
-				A(i) -= B(i);
-		}
-	}
-	return A;
-}
-
-
-
-template <class T>
-Fortran_Array1D<T>&  operator*=(Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=1; i<=n; i++)
-		{
-				A(i) *= B(i);
-		}
-	}
-	return A;
-}
-
-
-
-
-template <class T>
-Fortran_Array1D<T>&  operator/=(Fortran_Array1D<T> &A, const Fortran_Array1D<T> &B)
-{
-	int n = A.dim1();
-
-	if (B.dim1() == n)
-	{
-		for (int i=1; i<=n; i++)
-		{
-				A(i) /= B(i);
-		}
-	}
-	return A;
-}
-
-
-} // namespace TNT
-
-#endif
diff --git a/lib/include/tnt/tnt_fortran_array2d.h b/lib/include/tnt/tnt_fortran_array2d.h
deleted file mode 100644
index f307536..0000000
--- a/lib/include/tnt/tnt_fortran_array2d.h
+++ /dev/null
@@ -1,225 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT): Two-dimensional Fortran numerical array
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_FORTRAN_ARRAY2D_H
-#define TNT_FORTRAN_ARRAY2D_H
-
-#include <cstdlib>
-#include <iostream>
-
-#ifdef TNT_BOUNDS_CHECK
-#include <assert.h>
-#endif
-
-#include "tnt_i_refvec.h"
-
-namespace TNT
-{
-
-template <class T>
-class Fortran_Array2D 
-{
-
-
-  private: 
-  		i_refvec<T> v_;
-		int m_;
-		int n_;
-		T* data_;
-
-
-    	void initialize_(int n);
-    	void copy_(T* p, const T*  q, int len);
-    	void set_(T* begin,  T* end, const T& val);
- 
-  public:
-
-    typedef         T   value_type;
-
-	       Fortran_Array2D();
-	       Fortran_Array2D(int m, int n);
-	       Fortran_Array2D(int m, int n,  T *a);
-	       Fortran_Array2D(int m, int n, const T &a);
-    inline Fortran_Array2D(const Fortran_Array2D &A);
-	inline Fortran_Array2D & operator=(const T &a);
-	inline Fortran_Array2D & operator=(const Fortran_Array2D &A);
-	inline Fortran_Array2D & ref(const Fortran_Array2D &A);
-	       Fortran_Array2D copy() const;
-		   Fortran_Array2D & inject(const Fortran_Array2D & A);
-	inline T& operator()(int i, int j);
-	inline const T& operator()(int i, int j) const ;
-	inline int dim1() const;
-	inline int dim2() const;
-               ~Fortran_Array2D();
-
-	/* extended interface */
-
-	inline int ref_count() const;
-
-};
-
-template <class T>
-Fortran_Array2D<T>::Fortran_Array2D() : v_(), m_(0), n_(0), data_(0) {}
-
-
-template <class T>
-Fortran_Array2D<T>::Fortran_Array2D(const Fortran_Array2D<T> &A) : v_(A.v_),
-		m_(A.m_), n_(A.n_), data_(A.data_) {}
-
-
-
-template <class T>
-Fortran_Array2D<T>::Fortran_Array2D(int m, int n) : v_(m*n), m_(m), n_(n),
-	data_(v_.begin()) {}
-
-template <class T>
-Fortran_Array2D<T>::Fortran_Array2D(int m, int n, const T &val) : 
-	v_(m*n), m_(m), n_(n), data_(v_.begin())
-{
-	set_(data_, data_+m*n, val);
-}
-
-
-template <class T>
-Fortran_Array2D<T>::Fortran_Array2D(int m, int n, T *a) : v_(a),
-	m_(m), n_(n), data_(v_.begin()) {}
-
-
-
-
-template <class T>
-inline T& Fortran_Array2D<T>::operator()(int i, int j) 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i >= 1);
-	assert(i <= m_);
-	assert(j >= 1);
-	assert(j <= n_);
-#endif
-
-	return v_[ (j-1)*m_ + (i-1) ];
-
-}
-
-template <class T>
-inline const T& Fortran_Array2D<T>::operator()(int i, int j) const
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i >= 1);
-	assert(i <= m_);
-	assert(j >= 1);
-	assert(j <= n_);
-#endif
-
-	return v_[ (j-1)*m_ + (i-1) ];
-
-}
-
-
-template <class T>
-Fortran_Array2D<T> & Fortran_Array2D<T>::operator=(const T &a)
-{
- 	set_(data_, data_+m_*n_, a);
-	return *this;
-}
-
-template <class T>
-Fortran_Array2D<T> Fortran_Array2D<T>::copy() const
-{
-
-	Fortran_Array2D B(m_,n_);
-	
-	B.inject(*this);
-	return B;
-}
-
-
-template <class T>
-Fortran_Array2D<T> & Fortran_Array2D<T>::inject(const Fortran_Array2D &A)
-{
-	if (m_ == A.m_ && n_ == A.n_)
-		copy_(data_, A.data_, m_*n_);
-
-	return *this;
-}
-
-
-
-template <class T>
-Fortran_Array2D<T> & Fortran_Array2D<T>::ref(const Fortran_Array2D<T> &A)
-{
-	if (this != &A)
-	{
-		v_ = A.v_;
-		m_ = A.m_;
-		n_ = A.n_;
-		data_ = A.data_;
-	}
-	return *this;
-}
-
-template <class T>
-Fortran_Array2D<T> & Fortran_Array2D<T>::operator=(const Fortran_Array2D<T> &A)
-{
-	return ref(A);
-}
-
-template <class T>
-inline int Fortran_Array2D<T>::dim1() const { return m_; }
-
-template <class T>
-inline int Fortran_Array2D<T>::dim2() const { return n_; }
-
-
-template <class T>
-Fortran_Array2D<T>::~Fortran_Array2D()
-{
-}
-
-template <class T>
-inline int Fortran_Array2D<T>::ref_count() const { return v_.ref_count(); }
-
-
-
-
-template <class T>
-void Fortran_Array2D<T>::set_(T* begin, T* end, const T& a)
-{
-	for (T* p=begin; p<end; p++)
-		*p = a;
-
-}
-
-template <class T>
-void Fortran_Array2D<T>::copy_(T* p, const T* q, int len) 
-{
-	T *end = p + len;
-	while (p<end )
-		*p++ = *q++;
-
-}
-
-
-} /* namespace TNT */
-
-#endif
-/* TNT_FORTRAN_ARRAY2D_H */
-
diff --git a/lib/include/tnt/tnt_fortran_array2d_utils.h b/lib/include/tnt/tnt_fortran_array2d_utils.h
deleted file mode 100644
index bb68673..0000000
--- a/lib/include/tnt/tnt_fortran_array2d_utils.h
+++ /dev/null
@@ -1,236 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-#ifndef TNT_FORTRAN_ARRAY2D_UTILS_H
-#define TNT_FORTRAN_ARRAY2D_UTILS_H
-
-#include <iostream>
-
-namespace TNT
-{
-
-
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Fortran_Array2D<T> &A)
-{
-    int M=A.dim1();
-    int N=A.dim2();
-
-    s << M << " " << N << "\n";
-
-    for (int i=1; i<=M; i++)
-    {
-        for (int j=1; j<=N; j++)
-        {
-            s << A(i,j) << " ";
-        }
-        s << "\n";
-    }
-
-
-    return s;
-}
-
-template <class T>
-std::istream& operator>>(std::istream &s, Fortran_Array2D<T> &A)
-{
-
-    int M, N;
-
-    s >> M >> N;
-
-	Fortran_Array2D<T> B(M,N);
-
-    for (int i=1; i<=M; i++)
-        for (int j=1; j<=N; j++)
-        {
-            s >>  B(i,j);
-        }
-
-	A = B;
-    return s;
-}
-
-
-
-
-template <class T>
-Fortran_Array2D<T> operator+(const Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Fortran_Array2D<T>();
-
-	else
-	{
-		Fortran_Array2D<T> C(m,n);
-
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				C(i,j) = A(i,j) + B(i,j);
-		}
-		return C;
-	}
-}
-
-template <class T>
-Fortran_Array2D<T> operator-(const Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Fortran_Array2D<T>();
-
-	else
-	{
-		Fortran_Array2D<T> C(m,n);
-
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				C(i,j) = A(i,j) - B(i,j);
-		}
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array2D<T> operator*(const Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Fortran_Array2D<T>();
-
-	else
-	{
-		Fortran_Array2D<T> C(m,n);
-
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				C(i,j) = A(i,j) * B(i,j);
-		}
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array2D<T> operator/(const Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() != m ||  B.dim2() != n )
-		return Fortran_Array2D<T>();
-
-	else
-	{
-		Fortran_Array2D<T> C(m,n);
-
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				C(i,j) = A(i,j) / B(i,j);
-		}
-		return C;
-	}
-}
-
-
-
-template <class T>
-Fortran_Array2D<T>&  operator+=(Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				A(i,j) += B(i,j);
-		}
-	}
-	return A;
-}
-
-template <class T>
-Fortran_Array2D<T>&  operator-=(Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				A(i,j) -= B(i,j);
-		}
-	}
-	return A;
-}
-
-template <class T>
-Fortran_Array2D<T>&  operator*=(Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				A(i,j) *= B(i,j);
-		}
-	}
-	return A;
-}
-
-template <class T>
-Fortran_Array2D<T>&  operator/=(Fortran_Array2D<T> &A, const Fortran_Array2D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-
-	if (B.dim1() == m ||  B.dim2() == n )
-	{
-		for (int i=1; i<=m; i++)
-		{
-			for (int j=1; j<=n; j++)
-				A(i,j) /= B(i,j);
-		}
-	}
-	return A;
-}
-
-} // namespace TNT
-
-#endif
diff --git a/lib/include/tnt/tnt_fortran_array3d.h b/lib/include/tnt/tnt_fortran_array3d.h
deleted file mode 100644
index e51affb..0000000
--- a/lib/include/tnt/tnt_fortran_array3d.h
+++ /dev/null
@@ -1,223 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT): Three-dimensional Fortran numerical array
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_FORTRAN_ARRAY3D_H
-#define TNT_FORTRAN_ARRAY3D_H
-
-#include <cstdlib>
-#include <iostream>
-#ifdef TNT_BOUNDS_CHECK
-#include <assert.h>
-#endif
-#include "tnt_i_refvec.h"
-
-namespace TNT
-{
-
-template <class T>
-class Fortran_Array3D 
-{
-
-
-  private: 
-
-
-		i_refvec<T> v_;
-		int m_;
-		int n_;
-		int k_;
-		T* data_;
-
-  public:
-
-    typedef         T   value_type;
-
-	       Fortran_Array3D();
-	       Fortran_Array3D(int m, int n, int k);
-	       Fortran_Array3D(int m, int n, int k,  T *a);
-	       Fortran_Array3D(int m, int n, int k, const T &a);
-    inline Fortran_Array3D(const Fortran_Array3D &A);
-	inline Fortran_Array3D & operator=(const T &a);
-	inline Fortran_Array3D & operator=(const Fortran_Array3D &A);
-	inline Fortran_Array3D & ref(const Fortran_Array3D &A);
-	       Fortran_Array3D copy() const;
-		   Fortran_Array3D & inject(const Fortran_Array3D & A);
-	inline T& operator()(int i, int j, int k);
-	inline const T& operator()(int i, int j, int k) const ;
-	inline int dim1() const;
-	inline int dim2() const;
-	inline int dim3() const;
-	inline int ref_count() const;
-               ~Fortran_Array3D();
-
-
-};
-
-template <class T>
-Fortran_Array3D<T>::Fortran_Array3D() :  v_(), m_(0), n_(0), k_(0), data_(0) {}
-
-
-template <class T>
-Fortran_Array3D<T>::Fortran_Array3D(const Fortran_Array3D<T> &A) : 
-	v_(A.v_), m_(A.m_), n_(A.n_), k_(A.k_), data_(A.data_) {}
-
-
-
-template <class T>
-Fortran_Array3D<T>::Fortran_Array3D(int m, int n, int k) : 
-	v_(m*n*k), m_(m), n_(n), k_(k), data_(v_.begin()) {}
-
-
-
-template <class T>
-Fortran_Array3D<T>::Fortran_Array3D(int m, int n, int k, const T &val) : 
-	v_(m*n*k), m_(m), n_(n), k_(k), data_(v_.begin())
-{
-	for (T* p = data_; p < data_ + m*n*k; p++)
-		*p = val;
-}
-
-template <class T>
-Fortran_Array3D<T>::Fortran_Array3D(int m, int n, int k, T *a) : 
-	v_(a), m_(m), n_(n), k_(k), data_(v_.begin()) {}
-
-
-
-
-template <class T>
-inline T& Fortran_Array3D<T>::operator()(int i, int j, int k) 
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i >= 1);
-	assert(i <= m_);
-	assert(j >= 1);
-	assert(j <= n_);
-	assert(k >= 1);
-	assert(k <= k_);
-#endif
-
-	return data_[(k-1)*m_*n_ + (j-1) * m_ + i-1];
-
-}
-
-template <class T>
-inline const T& Fortran_Array3D<T>::operator()(int i, int j, int k)  const
-{ 
-#ifdef TNT_BOUNDS_CHECK
-	assert(i >= 1);
-	assert(i <= m_);
-	assert(j >= 1);
-	assert(j <= n_);
-	assert(k >= 1);
-	assert(k <= k_);
-#endif
-
-	return data_[(k-1)*m_*n_ + (j-1) * m_ + i-1];
-}
-
-
-template <class T>
-Fortran_Array3D<T> & Fortran_Array3D<T>::operator=(const T &a)
-{
-
-	T *end = data_ + m_*n_*k_;
-
-	for (T *p=data_; p != end; *p++ = a);
-
-	return *this;
-}
-
-template <class T>
-Fortran_Array3D<T> Fortran_Array3D<T>::copy() const
-{
-
-	Fortran_Array3D B(m_, n_, k_);
-	B.inject(*this);
-	return B;
-	
-}
-
-
-template <class T>
-Fortran_Array3D<T> & Fortran_Array3D<T>::inject(const Fortran_Array3D &A)
-{
-
-	if (m_ == A.m_ && n_ == A.n_ && k_ == A.k_)
-	{
-		T *p = data_;
-		T *end = data_ + m_*n_*k_;
-		const T* q = A.data_;
-		for (; p < end; *p++ =  *q++);
-	}
-	return *this;
-}
-
-
-
-
-template <class T>
-Fortran_Array3D<T> & Fortran_Array3D<T>::ref(const Fortran_Array3D<T> &A)
-{
-
-	if (this != &A)
-	{
-		v_ = A.v_;
-		m_ = A.m_;
-		n_ = A.n_;
-		k_ = A.k_;
-		data_ = A.data_;
-	}
-	return *this;
-}
-
-template <class T>
-Fortran_Array3D<T> & Fortran_Array3D<T>::operator=(const Fortran_Array3D<T> &A)
-{
-	return ref(A);
-}
-
-template <class T>
-inline int Fortran_Array3D<T>::dim1() const { return m_; }
-
-template <class T>
-inline int Fortran_Array3D<T>::dim2() const { return n_; }
-
-template <class T>
-inline int Fortran_Array3D<T>::dim3() const { return k_; }
-
-
-template <class T>
-inline int Fortran_Array3D<T>::ref_count() const 
-{ 
-	return v_.ref_count(); 
-}
-
-template <class T>
-Fortran_Array3D<T>::~Fortran_Array3D()
-{
-}
-
-
-} /* namespace TNT */
-
-#endif
-/* TNT_FORTRAN_ARRAY3D_H */
-
diff --git a/lib/include/tnt/tnt_fortran_array3d_utils.h b/lib/include/tnt/tnt_fortran_array3d_utils.h
deleted file mode 100644
index a13a275..0000000
--- a/lib/include/tnt/tnt_fortran_array3d_utils.h
+++ /dev/null
@@ -1,249 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-#ifndef TNT_FORTRAN_ARRAY3D_UTILS_H
-#define TNT_FORTRAN_ARRAY3D_UTILS_H
-
-#include <cstdlib>
-#include <cassert>
-
-namespace TNT
-{
-
-
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Fortran_Array3D<T> &A)
-{
-    int M=A.dim1();
-    int N=A.dim2();
-    int K=A.dim3();
-
-    s << M << " " << N << " " << K << "\n";
-
-    for (int i=1; i<=M; i++)
-    {
-        for (int j=1; j<=N; j++)
-        {
-			for (int k=1; k<=K; k++)
-            	s << A(i,j,k) << " ";
-			s << "\n";
-        }
-        s << "\n";
-    }
-
-
-    return s;
-}
-
-template <class T>
-std::istream& operator>>(std::istream &s, Fortran_Array3D<T> &A)
-{
-
-    int M, N, K;
-
-    s >> M >> N >> K;
-
-	Fortran_Array3D<T> B(M,N,K);
-
-    for (int i=1; i<=M; i++)
-        for (int j=1; j<=N; j++)
-			for (int k=1; k<=K; k++)
-            	s >>  B(i,j,k);
-
-	A = B;
-    return s;
-}
-
-
-template <class T>
-Fortran_Array3D<T> operator+(const Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Fortran_Array3D<T>();
-
-	else
-	{
-		Fortran_Array3D<T> C(m,n,p);
-
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-				C(i,j,k) = A(i,j,k)+ B(i,j,k);
-
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array3D<T> operator-(const Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Fortran_Array3D<T>();
-
-	else
-	{
-		Fortran_Array3D<T> C(m,n,p);
-
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-				C(i,j,k) = A(i,j,k)- B(i,j,k);
-
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array3D<T> operator*(const Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Fortran_Array3D<T>();
-
-	else
-	{
-		Fortran_Array3D<T> C(m,n,p);
-
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-				C(i,j,k) = A(i,j,k)* B(i,j,k);
-
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array3D<T> operator/(const Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() != m ||  B.dim2() != n || B.dim3() != p )
-		return Fortran_Array3D<T>();
-
-	else
-	{
-		Fortran_Array3D<T> C(m,n,p);
-
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-				C(i,j,k) = A(i,j,k)/ B(i,j,k);
-
-		return C;
-	}
-}
-
-
-template <class T>
-Fortran_Array3D<T>& operator+=(Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-					A(i,j,k) += B(i,j,k);
-	}
-
-	return A;
-}
-
-
-template <class T>
-Fortran_Array3D<T>& operator-=(Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-					A(i,j,k) -= B(i,j,k);
-	}
-
-	return A;
-}
-
-
-template <class T>
-Fortran_Array3D<T>& operator*=(Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-					A(i,j,k) *= B(i,j,k);
-	}
-
-	return A;
-}
-
-
-template <class T>
-Fortran_Array3D<T>& operator/=(Fortran_Array3D<T> &A, const Fortran_Array3D<T> &B)
-{
-	int m = A.dim1();
-	int n = A.dim2();
-	int p = A.dim3();
-
-	if (B.dim1() == m &&  B.dim2() == n && B.dim3() == p )
-	{
-		for (int i=1; i<=m; i++)
-			for (int j=1; j<=n; j++)
-				for (int k=1; k<=p; k++)
-					A(i,j,k) /= B(i,j,k);
-	}
-
-	return A;
-}
-
-
-} // namespace TNT
-
-#endif
diff --git a/lib/include/tnt/tnt_i_refvec.h b/lib/include/tnt/tnt_i_refvec.h
deleted file mode 100644
index 5a67eb5..0000000
--- a/lib/include/tnt/tnt_i_refvec.h
+++ /dev/null
@@ -1,243 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_I_REFVEC_H
-#define TNT_I_REFVEC_H
-
-#include <cstdlib>
-#include <iostream>
-
-#ifdef TNT_BOUNDS_CHECK
-#include <assert.h>
-#endif
-
-#ifndef NULL
-#define NULL 0
-#endif
-
-namespace TNT
-{
-/*
-	Internal representation of ref-counted array.  The TNT
-	arrays all use this building block.
-
-	<p>
-	If an array block is created by TNT, then every time 
-	an assignment is made, the left-hand-side reference 
-	is decreased by one, and the right-hand-side refernce
-	count is increased by one.  If the array block was
-	external to TNT, the refernce count is a NULL pointer
-	regardless of how many references are made, since the 
-	memory is not freed by TNT.
-
-
-	
-*/
-template <class T>
-class i_refvec
-{
-
-
-  private:
-    T* data_;                  
-    int *ref_count_;
-
-
-  public:
-
-			 i_refvec();
-	explicit i_refvec(int n);
-	inline	 i_refvec(T* data);
-	inline	 i_refvec(const i_refvec &v);
-	inline   T*		 begin();
-	inline const T* begin() const;
-	inline  T& operator[](int i);
-	inline const T& operator[](int i) const;
-	inline  i_refvec<T> & operator=(const i_refvec<T> &V);
-		    void copy_(T* p, const T* q, const T* e); 
-		    void set_(T* p, const T* b, const T* e); 
-	inline 	int	 ref_count() const;
-	inline  int is_null() const;
-	inline  void destroy();
-			 ~i_refvec();
-			
-};
-
-template <class T>
-void i_refvec<T>::copy_(T* p, const T* q, const T* e)
-{
-	for (T* t=p; q<e; t++, q++)
-		*t= *q;
-}
-
-template <class T>
-i_refvec<T>::i_refvec() : data_(NULL), ref_count_(NULL) {}
-
-/**
-	In case n is 0 or negative, it does NOT call new. 
-*/
-template <class T>
-i_refvec<T>::i_refvec(int n) : data_(NULL), ref_count_(NULL)
-{
-	if (n >= 1)
-	{
-#ifdef TNT_DEBUG
-		std::cout  << "new data storage.\n";
-#endif
-		data_ = new T[n];
-		ref_count_ = new int;
-		*ref_count_ = 1;
-	}
-}
-
-template <class T>
-inline	 i_refvec<T>::i_refvec(const i_refvec<T> &V): data_(V.data_),
-	ref_count_(V.ref_count_)
-{
-	if (V.ref_count_ != NULL)
-	    (*(V.ref_count_))++;
-}
-
-
-template <class T>
-i_refvec<T>::i_refvec(T* data) : data_(data), ref_count_(NULL) {}
-
-template <class T>
-inline T* i_refvec<T>::begin()
-{
-	return data_;
-}
-
-template <class T>
-inline const T& i_refvec<T>::operator[](int i) const
-{
-	return data_[i];
-}
-
-template <class T>
-inline T& i_refvec<T>::operator[](int i)
-{
-	return data_[i];
-}
-
-
-template <class T>
-inline const T* i_refvec<T>::begin() const
-{
-	return data_;
-}
-
-
-
-template <class T>
-i_refvec<T> & i_refvec<T>::operator=(const i_refvec<T> &V)
-{
-	if (this == &V)
-		return *this;
-
-
-	if (ref_count_ != NULL)
-	{
-		(*ref_count_) --;
-		if ((*ref_count_) == 0)
-			destroy();
-	}
-
-	data_ = V.data_;
-	ref_count_ = V.ref_count_;
-
-	if (V.ref_count_ != NULL)
-	    (*(V.ref_count_))++;
-
-	return *this;
-}
-
-template <class T>
-void i_refvec<T>::destroy()
-{
-	if (ref_count_ != NULL)
-	{
-#ifdef TNT_DEBUG
-		std::cout << "destorying data... \n";
-#endif
-		delete ref_count_;
-
-#ifdef TNT_DEBUG
-		std::cout << "deleted ref_count_ ...\n";
-#endif
-		if (data_ != NULL)
-			delete []data_;
-#ifdef TNT_DEBUG
-		std::cout << "deleted data_[] ...\n";
-#endif
-		data_ = NULL;
-	}
-}
-
-/*
-* return 1 is vector is empty, 0 otherwise
-*
-* if is_null() is false and ref_count() is 0, then
-* 
-*/
-template<class T>
-int i_refvec<T>::is_null() const
-{
-	return (data_ == NULL ? 1 : 0);
-}
-
-/*
-*  returns -1 if data is external, 
-*  returns 0 if a is NULL array,
-*  otherwise returns the positive number of vectors sharing
-*  		this data space.
-*/
-template <class T>
-int i_refvec<T>::ref_count() const
-{
-	if (data_ == NULL)
-		return 0;
-	else
-		return (ref_count_ != NULL ? *ref_count_ : -1) ; 
-}
-
-template <class T>
-i_refvec<T>::~i_refvec()
-{
-	if (ref_count_ != NULL)
-	{
-		(*ref_count_)--;
-
-		if (*ref_count_ == 0)
-		destroy();
-	}
-}
-
-
-} /* namespace TNT */
-
-
-
-
-
-#endif
-/* TNT_I_REFVEC_H */
-
diff --git a/lib/include/tnt/tnt_math_utils.h b/lib/include/tnt/tnt_math_utils.h
deleted file mode 100644
index f9c1c91..0000000
--- a/lib/include/tnt/tnt_math_utils.h
+++ /dev/null
@@ -1,34 +0,0 @@
-#ifndef MATH_UTILS_H
-#define MATH_UTILS_H
-
-/* needed for fabs, sqrt() below */
-#include <cmath>
-
-
-
-namespace TNT
-{
-/**
-	@returns hypotenuse of real (non-complex) scalars a and b by 
-	avoiding underflow/overflow
-	using (a * sqrt( 1 + (b/a) * (b/a))), rather than
-	sqrt(a*a + b*b).
-*/
-template <class Real>
-Real hypot(const Real &a, const Real &b)
-{
-	
-	if (a== 0)
-		return abs(b);
-	else
-	{
-		Real c = b/a;
-		return fabs(a) * sqrt(1 + c*c);
-	}
-}
-} /* TNT namespace */
-
-
-
-#endif
-/* MATH_UTILS_H */
diff --git a/lib/include/tnt/tnt_sparse_matrix_csr.h b/lib/include/tnt/tnt_sparse_matrix_csr.h
deleted file mode 100644
index 0d4fde1..0000000
--- a/lib/include/tnt/tnt_sparse_matrix_csr.h
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-#ifndef TNT_SPARSE_MATRIX_CSR_H
-#define TNT_SPARSE_MATRIX_CSR_H
-
-#include "tnt_array1d.h"
-
-namespace TNT
-{
-
-
-/**
-	Read-only view of a sparse matrix in compressed-row storage
-	format.  Neither array elements (nonzeros) nor sparsity
-	structure can be modified.  If modifications are required,
-	create a new view.
-
-	<p>
-	Index values begin at 0.
-
-	<p>
-	<b>Storage requirements:</b> An (m x n) matrix with
-	nz nonzeros requires no more than  ((T+I)*nz + M*I)
-	bytes, where T is the size of data elements and
-	I is the size of integers.
-	
-
-*/
-template <class T>
-class Sparse_Matrix_CompRow {
-
-private:
-	Array1D<T>    val_;       // data values (nz_ elements)
-    Array1D<int>  rowptr_;    // row_ptr (dim_[0]+1 elements)
-    Array1D<int>  colind_;    // col_ind  (nz_ elements)
-
-    int dim1_;        // number of rows
-    int dim2_;        // number of cols
-  
-public:
-
-	Sparse_Matrix_CompRow(const Sparse_Matrix_CompRow &S);
-	Sparse_Matrix_CompRow(int M, int N, int nz, const T *val, 
-						const int *r, const int *c);
-    
-
-
-    inline   const T&      val(int i) const { return val_[i]; }
-    inline   const int&         row_ptr(int i) const { return rowptr_[i]; }
-    inline   const int&         col_ind(int i) const { return colind_[i];}
-
-    inline   int    dim1() const {return dim1_;}
-    inline   int    dim2() const {return dim2_;}
-       int          NumNonzeros() const {return val_.dim1();}
-
-
-    Sparse_Matrix_CompRow& operator=(
-					const Sparse_Matrix_CompRow &R);
-
-
-
-};
-
-/**
-	Construct a read-only view of existing sparse matrix in
-	compressed-row storage format.
-
-	@param M the number of rows of sparse matrix
-	@param N the  number of columns of sparse matrix
-	@param nz the number of nonzeros
-	@param val a contiguous list of nonzero values
-	@param r row-pointers: r[i] denotes the begining position of row i
-		(i.e. the ith row begins at val[row[i]]).
-	@param c column-indices: c[i] denotes the column location of val[i]
-*/
-template <class T>
-Sparse_Matrix_CompRow<T>::Sparse_Matrix_CompRow(int M, int N, int nz,
-	const T *val, const int *r, const int *c) : val_(nz,val), 
-		rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
-
-
-}
-// namespace TNT
-
-#endif
diff --git a/lib/include/tnt/tnt_stopwatch.h b/lib/include/tnt/tnt_stopwatch.h
deleted file mode 100644
index 8dc5d23..0000000
--- a/lib/include/tnt/tnt_stopwatch.h
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain.  NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef STOPWATCH_H
-#define STOPWATCH_H
-
-// for clock() and CLOCKS_PER_SEC
-#include <time.h>
-
-
-namespace TNT
-{
-
-inline static double seconds(void)
-{
-    const double secs_per_tick = 1.0 / CLOCKS_PER_SEC;
-    return ( (double) clock() ) * secs_per_tick;
-}
-
-class Stopwatch {
-    private:
-        int running_;
-        double start_time_;
-        double total_;
-
-    public:
-        inline Stopwatch();
-        inline void start();
-        inline double stop();
-		inline double read();
-		inline void resume();
-		inline int running();
-};
-
-inline Stopwatch::Stopwatch() : running_(0), start_time_(0.0), total_(0.0) {}
-
-void Stopwatch::start() 
-{
-	running_ = 1;
-	total_ = 0.0;
-	start_time_ = seconds();
-}
-
-double Stopwatch::stop()  
-{
-	if (running_) 
-	{
-         total_ += (seconds() - start_time_); 
-         running_ = 0;
-    }
-    return total_; 
-}
-
-inline void Stopwatch::resume()
-{
-	if (!running_)
-	{
-		start_time_ = seconds();
-		running_ = 1;
-	}
-}
-		
-
-inline double Stopwatch::read()   
-{
-	if (running_)
-	{
-		stop();
-		resume();
-	}
-	return total_;
-}
-
-
-} /* TNT namespace */
-#endif
-    
-
-            
diff --git a/lib/include/tnt/tnt_subscript.h b/lib/include/tnt/tnt_subscript.h
deleted file mode 100644
index d8fe120..0000000
--- a/lib/include/tnt/tnt_subscript.h
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-#ifndef TNT_SUBSCRPT_H
-#define TNT_SUBSCRPT_H
-
-
-//---------------------------------------------------------------------
-// This definition describes the default TNT data type used for
-// indexing into TNT matrices and vectors.  The data type should
-// be wide enough to index into large arrays.  It defaults to an
-// "int", but can be overriden at compile time redefining TNT_SUBSCRIPT_TYPE,
-// e.g.
-// 
-//      c++ -DTNT_SUBSCRIPT_TYPE='unsigned int'  ...
-//
-//---------------------------------------------------------------------
-//
-
-#ifndef TNT_SUBSCRIPT_TYPE
-#define TNT_SUBSCRIPT_TYPE int
-#endif
-
-namespace TNT
-{
-    typedef TNT_SUBSCRIPT_TYPE Subscript;
-} /* namespace TNT */
-
-
-// () indexing in TNT means 1-offset, i.e. x(1) and A(1,1) are the
-// first elements.  This offset is left as a macro for future
-// purposes, but should not be changed in the current release.
-//
-//
-#define TNT_BASE_OFFSET (1)
-
-#endif
diff --git a/lib/include/tnt/tnt_vec.h b/lib/include/tnt/tnt_vec.h
deleted file mode 100644
index 3455d79..0000000
--- a/lib/include/tnt/tnt_vec.h
+++ /dev/null
@@ -1,404 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-
-
-#ifndef TNT_VEC_H
-#define TNT_VEC_H
-
-#include "tnt_subscript.h"
-#include <cstdlib>
-#include <cassert>
-#include <iostream>
-#include <sstream>
-
-namespace TNT
-{
-
-/**
- <b>[Deprecatred]</b>  Value-based vector class from pre-1.0
- 	TNT version.  Kept here for backward compatiblity, but should
-	use the newer TNT::Array1D classes instead.
-
-*/
-
-template <class T>
-class Vector 
-{
-
-
-  public:
-
-    typedef Subscript   size_type;
-    typedef         T   value_type;
-    typedef         T   element_type;
-    typedef         T*  pointer;
-    typedef         T*  iterator;
-    typedef         T&  reference;
-    typedef const   T*  const_iterator;
-    typedef const   T&  const_reference;
-
-    Subscript lbound() const { return 1;}
- 
-  protected:
-    T* v_;                  
-    T* vm1_;        // pointer adjustment for optimzied 1-offset indexing
-    Subscript n_;
-
-    // internal helper function to create the array
-    // of row pointers
-
-    void initialize(Subscript N)
-    {
-        // adjust pointers so that they are 1-offset:
-        // v_[] is the internal contiguous array, it is still 0-offset
-        //
-        assert(v_ == NULL);
-        v_ = new T[N];
-        assert(v_  != NULL);
-        vm1_ = v_-1;
-        n_ = N;
-    }
-   
-    void copy(const T*  v)
-    {
-        Subscript N = n_;
-        Subscript i;
-
-#ifdef TNT_UNROLL_LOOPS
-        Subscript Nmod4 = N & 3;
-        Subscript N4 = N - Nmod4;
-
-        for (i=0; i<N4; i+=4)
-        {
-            v_[i] = v[i];
-            v_[i+1] = v[i+1];
-            v_[i+2] = v[i+2];
-            v_[i+3] = v[i+3];
-        }
-
-        for (i=N4; i< N; i++)
-            v_[i] = v[i];
-#else
-
-        for (i=0; i< N; i++)
-            v_[i] = v[i];
-#endif      
-    }
-
-    void set(const T& val)
-    {
-        Subscript N = n_;
-        Subscript i;
-
-#ifdef TNT_UNROLL_LOOPS
-        Subscript Nmod4 = N & 3;
-        Subscript N4 = N - Nmod4;
-
-        for (i=0; i<N4; i+=4)
-        {
-            v_[i] = val;
-            v_[i+1] = val;
-            v_[i+2] = val;
-            v_[i+3] = val; 
-        }
-
-        for (i=N4; i< N; i++)
-            v_[i] = val;
-#else
-
-        for (i=0; i< N; i++)
-            v_[i] = val;
-        
-#endif      
-    }
-    
-
-
-    void destroy()
-    {     
-        /* do nothing, if no memory has been previously allocated */
-        if (v_ == NULL) return ;
-
-        /* if we are here, then matrix was previously allocated */
-        delete [] (v_);     
-
-        v_ = NULL;
-        vm1_ = NULL;
-    }
-
-
-  public:
-
-    // access
-
-    iterator begin() { return v_;}
-    iterator end()   { return v_ + n_; }
-    const iterator begin() const { return v_;}
-    const iterator end() const  { return v_ + n_; }
-
-    // destructor
-
-    ~Vector() 
-    {
-        destroy();
-    }
-
-    // constructors
-
-    Vector() : v_(0), vm1_(0), n_(0)  {};
-
-    Vector(const Vector<T> &A) : v_(0), vm1_(0), n_(0)
-    {
-        initialize(A.n_);
-        copy(A.v_);
-    }
-
-    Vector(Subscript N, const T& value = T()) :  v_(0), vm1_(0), n_(0)
-    {
-        initialize(N);
-        set(value);
-    }
-
-    Vector(Subscript N, const T* v) :  v_(0), vm1_(0), n_(0)
-    {
-        initialize(N);
-        copy(v);
-    }
-
-    Vector(Subscript N, char *s) :  v_(0), vm1_(0), n_(0)
-    {
-        initialize(N);
-        std::istringstream ins(s);
-
-        Subscript i;
-
-        for (i=0; i<N; i++)
-                ins >> v_[i];
-    }
-
-
-    // methods
-    // 
-    Vector<T>& newsize(Subscript N)
-    {
-        if (n_ == N) return *this;
-
-        destroy();
-        initialize(N);
-
-        return *this;
-    }
-
-
-    // assignments
-    //
-    Vector<T>& operator=(const Vector<T> &A)
-    {
-        if (v_ == A.v_)
-            return *this;
-
-        if (n_ == A.n_)         // no need to re-alloc
-            copy(A.v_);
-
-        else
-        {
-            destroy();
-            initialize(A.n_);
-            copy(A.v_);
-        }
-
-        return *this;
-    }
-        
-    Vector<T>& operator=(const T& scalar)
-    { 
-        set(scalar);  
-        return *this;
-    }
-
-    inline Subscript dim() const 
-    {
-        return  n_; 
-    }
-
-    inline Subscript size() const 
-    {
-        return  n_; 
-    }
-
-
-    inline reference operator()(Subscript i)
-    { 
-#ifdef TNT_BOUNDS_CHECK
-        assert(1<=i);
-        assert(i <= n_) ;
-#endif
-        return vm1_[i]; 
-    }
-
-    inline const_reference operator() (Subscript i) const
-    {
-#ifdef TNT_BOUNDS_CHECK
-        assert(1<=i);
-        assert(i <= n_) ;
-#endif
-        return vm1_[i]; 
-    }
-
-    inline reference operator[](Subscript i)
-    { 
-#ifdef TNT_BOUNDS_CHECK
-        assert(0<=i);
-        assert(i < n_) ;
-#endif
-        return v_[i]; 
-    }
-
-    inline const_reference operator[](Subscript i) const
-    {
-#ifdef TNT_BOUNDS_CHECK
-        assert(0<=i);
-
-
-
-
-
-
-        assert(i < n_) ;
-#endif
-        return v_[i]; 
-    }
-
-
-
-};
-
-
-/* ***************************  I/O  ********************************/
-
-template <class T>
-std::ostream& operator<<(std::ostream &s, const Vector<T> &A)
-{
-    Subscript N=A.dim();
-
-    s <<  N << "\n";
-
-    for (Subscript i=0; i<N; i++)
-        s   << A[i] << " " << "\n";
-    s << "\n";
-
-    return s;
-}
-
-template <class T>
-std::istream & operator>>(std::istream &s, Vector<T> &A)
-{
-
-    Subscript N;
-
-    s >> N;
-
-    if ( !(N == A.size() ))
-    {
-        A.newsize(N);
-    }
-
-
-    for (Subscript i=0; i<N; i++)
-            s >>  A[i];
-
-
-    return s;
-}
-
-// *******************[ basic matrix algorithms ]***************************
-
-
-template <class T>
-Vector<T> operator+(const Vector<T> &A, 
-    const Vector<T> &B)
-{
-    Subscript N = A.dim();
-
-    assert(N==B.dim());
-
-    Vector<T> tmp(N);
-    Subscript i;
-
-    for (i=0; i<N; i++)
-            tmp[i] = A[i] + B[i];
-
-    return tmp;
-}
-
-template <class T>
-Vector<T> operator-(const Vector<T> &A, 
-    const Vector<T> &B)
-{
-    Subscript N = A.dim();
-
-    assert(N==B.dim());
-
-    Vector<T> tmp(N);
-    Subscript i;
-
-    for (i=0; i<N; i++)
-            tmp[i] = A[i] - B[i];
-
-    return tmp;
-}
-
-template <class T>
-Vector<T> operator*(const Vector<T> &A, 
-    const Vector<T> &B)
-{
-    Subscript N = A.dim();
-
-    assert(N==B.dim());
-
-    Vector<T> tmp(N);
-    Subscript i;
-
-    for (i=0; i<N; i++)
-            tmp[i] = A[i] * B[i];
-
-    return tmp;
-}
-
-
-template <class T>
-T dot_prod(const Vector<T> &A, const Vector<T> &B)
-{
-    Subscript N = A.dim();
-    assert(N == B.dim());
-
-    Subscript i;
-    T sum = 0;
-
-    for (i=0; i<N; i++)
-        sum += A[i] * B[i];
-
-    return sum;
-}
-
-}   /* namespace TNT */
-
-#endif
-// TNT_VEC_H
diff --git a/lib/include/tnt/tnt_version.h b/lib/include/tnt/tnt_version.h
deleted file mode 100644
index 047e7d3..0000000
--- a/lib/include/tnt/tnt_version.h
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
-*
-* Template Numerical Toolkit (TNT)
-*
-* Mathematical and Computational Sciences Division
-* National Institute of Technology,
-* Gaithersburg, MD USA
-*
-*
-* This software was developed at the National Institute of Standards and
-* Technology (NIST) by employees of the Federal Government in the course
-* of their official duties. Pursuant to title 17 Section 105 of the
-* United States Code, this software is not subject to copyright protection
-* and is in the public domain. NIST assumes no responsibility whatsoever for
-* its use by other parties, and makes no guarantees, expressed or implied,
-* about its quality, reliability, or any other characteristic.
-*
-*/
-
-#ifndef TNT_VERSION_H
-#define TNT_VERSION_H
-
-
-//---------------------------------------------------------------------
-//  current version 
-//---------------------------------------------------------------------
-
-
-#define TNT_MAJOR_VERSION    '1'
-#define TNT_MINOR_VERSION    '2'
-#define TNT_SUBMINOR_VERSION '6'
-#define TNT_VERSION_STRING "1.2.6"
-
-
-
-
-
-#endif
-// TNT_VERSION_H
diff --git a/lib/licenses/tnt.txt b/lib/licenses/tnt.txt
deleted file mode 100644
index 3dafbe0..0000000
--- a/lib/licenses/tnt.txt
+++ /dev/null
@@ -1,14 +0,0 @@
-Template Numerical Toolkit (TNT): Linear Algebra Module
-
-Mathematical and Computational Sciences Division
-National Institute of Technology,
-Gaithersburg, MD USA
-
-
-This software was developed at the National Institute of Standards and
-Technology (NIST) by employees of the Federal Government in the course
-of their official duties. Pursuant to title 17 Section 105 of the
-United States Code, this software is not subject to copyright protection
-and is in the public domain. NIST assumes no responsibility whatsoever for
-its use by other parties, and makes no guarantees, expressed or implied,
-about its quality, reliability, or any other characteristic.