Index: src/LinearAlgebra/Makefile.am
===================================================================
--- src/LinearAlgebra/Makefile.am	(revision 8e9ce1f9895161c968ecfcdfd3228bebdd711671)
+++ src/LinearAlgebra/Makefile.am	(revision ef0c6bec93c0171ad946293a423b49bee2708b58)
@@ -12,5 +12,4 @@
   ${HELPERSOURCE} \
   BoxVector.cpp \
-  gslvector.cpp \
   Line.cpp \
   LineSegment.cpp \
@@ -28,5 +27,4 @@
 LINALGHEADER = \
   BoxVector.hpp \
-  gslvector.hpp \
   Line.hpp \
   LineSegment.hpp \
Index: c/LinearAlgebra/gslvector.cpp
===================================================================
--- src/LinearAlgebra/gslvector.cpp	(revision 8e9ce1f9895161c968ecfcdfd3228bebdd711671)
+++ 	(revision )
@@ -1,319 +1,0 @@
-/*
- * Project: MoleCuilder
- * Description: creates and alters molecular systems
- * Copyright (C)  2010 University of Bonn. All rights reserved.
- * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
- */
-
-/*
- * gslvector.cpp
- *
- *  Created on: Jan 8, 2010
- *      Author: heber
- */
-
-// include config.h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "Helpers/MemDebug.hpp"
-
-#include <cassert>
-#include <cmath>
-#include <iostream>
-
-#include "LinearAlgebra/gslvector.hpp"
-#include "defs.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "VectorContent.hpp"
-
-/** Constructor of class GSLVector.
- * Allocates GSL structures
- * \param m dimension of vector
- */
-GSLVector::GSLVector(size_t m) : dimension(m)
-{
-  vector = gsl_vector_calloc(dimension);
-};
-
-/** Copy constructor of class GSLVector.
- * Allocates GSL structures and copies components from \a *src.
- * \param *src source vector
- */
-GSLVector::GSLVector(const GSLVector * const src) : dimension(src->dimension)
-{
-  vector = gsl_vector_alloc(dimension);
-  gsl_vector_memcpy (vector, src->vector);
-};
-
-/** Copy constructor of class GSLVector.
- * Allocates GSL structures and copies components from \a *src.
- * \param *src source vector
- */
-GSLVector::GSLVector(const GSLVector & src) : dimension(src.dimension)
-{
-  vector = gsl_vector_alloc(dimension);
-  gsl_vector_memcpy (vector, src.vector);
-};
-
-/** Destructor of class GSLVector.
- * Frees GSL structures
- */
-GSLVector::~GSLVector()
-{
-  gsl_vector_free(vector);
-};
-
-/* ============================ Accessing =============================== */
-/** This function sets the vector from a double array.
- * Creates a vector view of the array and performs a memcopy.
- * \param *x array of values (no dimension check is performed)
- */
-void GSLVector::SetFromDoubleArray(double * x)
-{
-  gsl_vector_view m = gsl_vector_view_array (x, dimension);
-  gsl_vector_memcpy (vector, &m.vector);
-};
-
-/**
- * This function sets the GSLvector from an ordinary vector.
- *
- * Takes access to the internal gsl_vector and copies it
- */
-void GSLVector::SetFromVector(Vector &v){
-  gsl_vector_memcpy (vector, v.get()->content);
-}
-
-/** This function returns the i-th element of a vector.
- * If \a m lies outside the allowed range of 0 to GSLVector::dimension-1 then the error handler is invoked and 0 is returned.
- * \param m m-th element
- * \return  m-th element of vector
- */
-double GSLVector::Get(size_t m) const
-{
-  return gsl_vector_get (vector, m);
-};
-
-/** This function sets the value of the \a m -th element of a vector to \a x.
- *  If \a m lies outside the allowed range of 0 to GSLVector::dimension-1 then the error handler is invoked.
- * \param m-th element to set
- * \param x value to set to
- */
-void GSLVector::Set(size_t m, double x)
-{
-  gsl_vector_set (vector, m, x);
-};
-
-/** These functions return a pointer to the \a m-th element of a vector.
- *  If \a m lies outside the allowed range of 0 to GSLVector::dimension-1 then the error handler is invoked and a null pointer is returned.
- * \param m m-th element
- * \return pointer to \a m-th element
- */
-double *GSLVector::Pointer(size_t m) const
-{
-  return gsl_vector_ptr (vector, m);
-};
-
-/** These functions return a constant pointer to the \a m-th element of a vector.
- *  If \a m lies outside the allowed range of 0 to GSLVector::dimension-1 then the error handler is invoked and a null pointer is returned.
- * \param m m-th element
- * \return const pointer to \a m-th element
- */
-const double *GSLVector::const_Pointer(size_t m) const
-{
-  return gsl_vector_const_ptr (vector, m);
-};
-
-/** Returns the dimension of the vector.
- * \return dimension of vector
- */
-#ifdef HAVE_INLINE
-inline
-#endif
-size_t GSLVector::GetDimension() const
-{
-  return dimension;
-};
-
-/* ========================== Initializing =============================== */
-/** This function sets all the elements of the vector to the value \a x.
- * \param *x
- */
-void GSLVector::SetAll(double x)
-{
-  gsl_vector_set_all (vector, x);
-};
-
-/** This function sets all the elements of the vector to zero.
- */
-void GSLVector::SetZero()
-{
-  gsl_vector_set_zero (vector);
-};
-
-/** This function makes a basis vector by setting all the elements of the vector to zero except for the i-th element which is set to one.
- * \param i i-th component to set to unity (all other to zero)
- * \return vector set
- */
-int GSLVector::SetBasis(size_t i)
-{
-  return gsl_vector_set_basis (vector, i);
-};
-
-/* ====================== Exchanging elements ============================ */
-/** This function exchanges the \a i-th and \a j-th elements of the vector in-place.
- * \param i i-th element to swap with ...
- * \param j ... j-th element to swap against
- */
-int GSLVector::SwapElements(size_t i, size_t j)
-{
-  return gsl_vector_swap_elements (vector, i, j);
-};
-
-/** This function reverses the order of the elements of the vector.
- */
-int GSLVector::Reverse()
-{
-  return gsl_vector_reverse (vector);
-};
-
-
-/* ========================== Operators =============================== */
-/** Compares GSLVector \a to GSLVector \a b component-wise.
- * \param a base GSLVector
- * \param b GSLVector components to add
- * \return a == b
- */
-bool operator==(const GSLVector& a, const GSLVector& b)
-{
-  bool status = true;
-  assert(a.GetDimension() == b.GetDimension() && "Dimenions of GSLVectors to compare differ");
-  for (size_t i=0;i<a.GetDimension();i++)
-    status = status && (fabs(a.Get(i) - b.Get(i)) < MYEPSILON);
-  return status;
-};
-
-/** Sums GSLVector \a to this lhs component-wise.
- * \param a base GSLVector
- * \param b GSLVector components to add
- * \return lhs + a
- */
-const GSLVector& operator+=(GSLVector& a, const GSLVector& b)
-{
-  assert(a.GetDimension() == b.GetDimension() && "Dimenions of GSLVectors to compare differ");
-  for (size_t i=0;i<a.GetDimension();i++)
-    a.Set(i,a.Get(i)+b.Get(i));
-  return a;
-};
-
-/** Subtracts GSLVector \a from this lhs component-wise.
- * \param a base GSLVector
- * \param b GSLVector components to add
- * \return lhs - a
- */
-const GSLVector& operator-=(GSLVector& a, const GSLVector& b)
-{
-  assert(a.GetDimension() == b.GetDimension() && "Dimenions of GSLVectors to compare differ");
-  for (size_t i=0;i<a.GetDimension();i++)
-    a.Set(i,a.Get(i)-b.Get(i));
-  return a;
-};
-
-/** factor each component of \a a times a double \a m.
- * \param a base GSLVector
- * \param m factor
- * \return lhs.Get(i) * m
- */
-const GSLVector& operator*=(GSLVector& a, const double m)
-{
-  for (size_t i=0;i<a.GetDimension();i++)
-    a.Set(i,a.Get(i)*m);
-  return a;
-};
-
-/** Sums two GSLVectors \a  and \b component-wise.
- * \param a first GSLVector
- * \param b second GSLVector
- * \return a + b
- */
-GSLVector const operator+(const GSLVector& a, const GSLVector& b)
-{
-  GSLVector x(a);
-  for (size_t i=0;i<a.GetDimension();i++)
-    x.Set(i,a.Get(i)+b.Get(i));
-  return x;
-};
-
-/** Subtracts GSLVector \a from \b component-wise.
- * \param a first GSLVector
- * \param b second GSLVector
- * \return a - b
- */
-GSLVector const operator-(const GSLVector& a, const GSLVector& b)
-{
-  assert(a.GetDimension() == b.GetDimension() && "Dimenions of GSLVectors to compare differ");
-  GSLVector x(a);
-  for (size_t i=0;i<a.GetDimension();i++)
-    x.Set(i,a.Get(i)-b.Get(i));
-  return x;
-};
-
-/** Factors given GSLVector \a a times \a m.
- * \param a GSLVector
- * \param m factor
- * \return m * a
- */
-GSLVector const operator*(const GSLVector& a, const double m)
-{
-  GSLVector x(a);
-  for (size_t i=0;i<a.GetDimension();i++)
-    x.Set(i,a.Get(i)*m);
-  return x;
-};
-
-/** Factors given GSLVector \a a times \a m.
- * \param m factor
- * \param a GSLVector
- * \return m * a
- */
-GSLVector const operator*(const double m, const GSLVector& a )
-{
-  GSLVector x(a);
-  for (size_t i=0;i<a.GetDimension();i++)
-    x.Set(i,a.Get(i)*m);
-  return x;
-};
-
-ostream& operator<<(ostream& ost, const GSLVector& m)
-{
-  ost << "(";
-  for (size_t i=0;i<m.GetDimension();i++) {
-    ost << m.Get(i);
-    if (i != 2)
-      ost << ",";
-  }
-  ost << ")";
-  return ost;
-};
-
-/* ====================== Checking State ============================ */
-/** Checks whether vector has all components zero.
- * @return true - vector is zero, false - vector is not
- */
-bool GSLVector::IsZero() const
-{
-  return (fabs(Get(0))+fabs(Get(1))+fabs(Get(2)) < MYEPSILON);
-};
-
-/** Checks whether vector has length of 1.
- * @return true - vector is normalized, false - vector is not
- */
-bool GSLVector::IsOne() const
-{
-  double NormValue = 0.;
-  for (size_t i=dimension;--i;)
-    NormValue += Get(i)*Get(i);
-  return (fabs(NormValue - 1.) < MYEPSILON);
-};
-
Index: c/LinearAlgebra/gslvector.hpp
===================================================================
--- src/LinearAlgebra/gslvector.hpp	(revision 8e9ce1f9895161c968ecfcdfd3228bebdd711671)
+++ 	(revision )
@@ -1,80 +1,0 @@
-/*
- * gslvector.hpp
- *
- *  Created on: Jan 8, 2010
- *      Author: heber
- */
-
-#ifndef GSLVECTOR_HPP_
-#define GSLVECTOR_HPP_
-
-using namespace std;
-
-/*********************************************** includes ***********************************/
-
-// include config.h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <iosfwd>
-#include <gsl/gsl_vector.h>
-
-/****************************************** forward declarations *****************************/
-
-class GSLVector;
-class Vector;
-
-/********************************************** declarations *******************************/
-
-class GSLVector {
-  friend class LinearSystemOfEquations;
-
-public:
-  GSLVector(size_t m);
-  GSLVector(const GSLVector * const src);
-  GSLVector(const GSLVector & src);
-  ~GSLVector();
-
-  // Accessing
-  void SetFromDoubleArray(double *x);
-  void SetFromVector(Vector &v);
-  double Get(size_t m) const;
-  void Set(size_t m, double x);
-  double *Pointer(size_t m) const;
-  const double *const_Pointer(size_t m) const;
-  size_t GetDimension() const;
-
-  // Initializing
-  void SetAll(double x);
-  void SetZero();
-  int SetBasis(size_t m);
-
-  // Exchanging elements
-  int SwapElements(size_t i, size_t j);
-  int Reverse();
-
-  // checking state
-  bool IsZero() const;
-  bool IsOne() const;
-
-private:
-  gsl_vector *vector;
-
-  const size_t dimension;
-};
-
-ostream & operator << (ostream& ost, const GSLVector &m);
-bool operator==(const GSLVector& a, const GSLVector& b);
-const GSLVector& operator+=(GSLVector& a, const GSLVector& b);
-const GSLVector& operator-=(GSLVector& a, const GSLVector& b);
-const GSLVector& operator*=(GSLVector& a, const double m);
-GSLVector const operator*(const GSLVector& a, const double m);
-GSLVector const operator*(const double m, const GSLVector& a);
-GSLVector const operator+(const GSLVector& a, const GSLVector& b);
-GSLVector const operator-(const GSLVector& a, const GSLVector& b);
-
-
-
-
-#endif /* GSLVECTOR_HPP_ */
