Created reference implementation of rigid shake algorithm. Added the JAMA package to OpenMM.

CMakeLists.txt

@@ -51,7 +51,7 @@ SUBDIRS (tests)
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
-SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla platforms/reference)
+SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla jama platforms/reference)
 
 # The build system will set ARCH64 for 64 bit builds, which require
 # use of the lib64/ library directories rather than lib/.

jama/include/jama_cholesky.h

+#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

jama/include/jama_lu.h

+#ifndef JAMA_LU_H
+#define JAMA_LU_H
+
+#include "tnt.h"
+#include <algorithm>
+//for min(), max() below
+
+using namespace TNT;
+using namespace std;
+
+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 = 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 */

jama/include/jama_qr.h

+#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
+

jama/include/jama_svd.h

+#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;
+
+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 = min(m,n);
+      s = Array1D<Real>(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 = min(m-1,n);
+      int nrt = max(0,min(n-2,m));
+      for (k = 0; k < 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 = 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 = max(max(max(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 = 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[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 = 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

jama/include/tnt.h

+/*
+*
+* 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

jama/include/tnt_array1d.h

+/*
+*
+* 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 */
+

jama/include/tnt_array1d_utils.h

+/*
+*
+* 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

jama/include/tnt_array2d.h

+/*
+*
+* 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 */
+

jama/include/tnt_array2d_utils.h

+/*
+*
+* 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

jama/include/tnt_array3d.h

+/*
+*
+* 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 */
+

jama/include/tnt_array3d_utils.h

+
+
+#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

jama/include/tnt_cmat.h

+/*
+*
+* 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

jama/include/tnt_fortran_array2d.h

+/*
+*
+* 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 */
+