Changeset 6c438f for src/LinearAlgebra

Timestamp:

Aug 28, 2010, 3:21:11 AM (15 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

a6e6b5, f8982c

Parents:

2ad482 (diff), fd4905 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (08/28/10 03:17:48)

git-committer:

Frederik Heber <heber@…> (08/28/10 03:21:11)

Message:

Merge branch 'StructureRefactoring' into Shapes

Conflicts:

src/Box.cpp
src/Box.hpp
src/Descriptors/AtomShapeDescriptor.cpp
src/Descriptors/AtomShapeDescriptor.hpp
src/Descriptors/AtomShapeDescriptor_impl.hpp
src/LinearAlgebra/Line.cpp
src/LinearAlgebra/Line.hpp
src/LinearAlgebra/Matrix.cpp
src/LinearAlgebra/Matrix.hpp
src/Makefile.am
src/Shapes/BaseShapes.cpp
src/Shapes/BaseShapes_impl.hpp
src/Shapes/Shape.cpp
src/Shapes/Shape.hpp
src/Shapes/ShapeOps_impl.hpp
src/Shapes/Shape_impl.hpp
src/unittests/ShapeUnittest.cpp

• AtomShapeDescriptor had been implemented doubly.
• LineSegment* moved to LinearAlgebra/
• BaseShapes:: Cuboid is from (0,0,0) and not from (-1,-1,-1) to (1,1,1)
  • had to fix ShapeUnittest
• some overlap in Shapes due to getHomogeneousPointsOnSurface added in stable.
• BUGFIX: Matrix::transpose() did not allocate MatrixContent::content.
• merged BaseShapesUnitTest into ShapeUnitTest.

Location:

src/LinearAlgebra

Files:

• BoxVector.cpp (added)
• BoxVector.hpp (added)
• Line.cpp (moved) (moved from src/Line.cpp ) (4 diffs)
• Line.hpp (moved) (moved from src/Line.hpp ) (2 diffs)
• LineSegment.cpp (moved) (moved from src/LineSegment.cpp ) (1 diff)
• LineSegment.hpp (moved) (moved from src/LineSegment.hpp )
• LineSegmentSet.cpp (moved) (moved from src/LineSegmentSet.cpp ) (1 diff)
• LineSegmentSet.hpp (moved) (moved from src/LineSegmentSet.hpp )
• Makefile.am (added)
• Matrix.cpp (moved) (moved from src/Matrix.cpp ) (11 diffs)
• Matrix.hpp (moved) (moved from src/Matrix.hpp ) (3 diffs)
• MatrixContent.hpp (moved) (moved from src/MatrixContent.hpp )
• Plane.cpp (moved) (moved from src/Plane.cpp ) (2 diffs)
• Plane.hpp (moved) (moved from src/Plane.hpp ) (1 diff)
• Space.cpp (moved) (moved from src/Space.cpp ) (2 diffs)
• Space.hpp (moved) (moved from src/Space.hpp )
• Vector.cpp (moved) (moved from src/vector.cpp ) (5 diffs)
• Vector.hpp (moved) (moved from src/vector.hpp ) (3 diffs)
• VectorContent.hpp (moved) (moved from src/VectorContent.hpp ) (1 diff)
• VectorInterface.cpp (added)
• VectorInterface.hpp (added)
• VectorSet.hpp (moved) (moved from src/VectorSet.hpp ) (1 diff)
• gslmatrix.cpp (moved) (moved from src/gslmatrix.cpp ) (2 diffs)
• gslmatrix.hpp (moved) (moved from src/gslmatrix.hpp )
• gslvector.cpp (moved) (moved from src/gslvector.cpp ) (3 diffs)
• gslvector.hpp (moved) (moved from src/gslvector.hpp )
• linearsystemofequations.cpp (moved) (moved from src/linearsystemofequations.cpp ) (2 diffs)
• linearsystemofequations.hpp (moved) (moved from src/linearsystemofequations.hpp ) (2 diffs)
• vector_ops.cpp (moved) (moved from src/vector_ops.cpp ) (2 diffs)
• vector_ops.hpp (moved) (moved from src/vector_ops.hpp )

src/LinearAlgebra/Line.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /*
  * Line.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
-#include "Line.hpp"
+#include "LinearAlgebra/Line.hpp"
 
 #include <cmath>
-
-#include "vector.hpp"
-#include "log.hpp"
-#include "verbose.hpp"
-#include "gslmatrix.hpp"
-#include "info.hpp"
+#include <iostream>
+
+#include "LinearAlgebra/Vector.hpp"
+#include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
+#include "LinearAlgebra/gslmatrix.hpp"
+#include "Helpers/Info.hpp"
 #include "Exceptions/LinearDependenceException.hpp"
 #include "Exceptions/SkewException.hpp"
-#include "Plane.hpp"
+#include "LinearAlgebra/Plane.hpp"
 
 using namespace std;
@@ -294 +307 @@
 }
 
-
 /******************************** Points on the line ********************/
 
@@ -339 +351 @@
   return x.param<y.param;
 }
+
+ostream& operator<<(ostream& ost, const Line& m)
+{
+  const Vector origin = m.getOrigin();
+  const Vector direction = m.getDirection();
+  ost << "(";
+  for (int i=0;i<NDIM;i++) {
+    ost << origin[i];
+    if (i != 2)
+      ost << ",";
+  }
+  ost << ") -> (";
+  for (int i=0;i<NDIM;i++) {
+    ost << direction[i];
+    if (i != 2)
+      ost << ",";
+  }
+  ost << ")";
+  return ost;
+};
+

src/LinearAlgebra/Line.hpp

@@ -9 +9 @@
 #define LINE_HPP_
 
-#include "Space.hpp"
+#include "LinearAlgebra/Space.hpp"
 
+#include <iosfwd>
 #include <memory>
 #include <vector>
@@ -60 +61 @@
 bool operator==(const Line&,const Line&);
 
+std::ostream & operator << (std::ostream& ost, const Line &m);
+
 /**
  * Named constructor to make a line through two points

src/LinearAlgebra/LineSegment.cpp

@@ -6 +6 @@
  */
 
-#include "LineSegment.hpp"
+#include "LinearAlgebra/LineSegment.hpp"
 #include "Helpers/Assert.hpp"
 
 #include "Line.hpp"
-#include "vector.hpp"
+#include "LinearAlgebra/Vector.hpp"
 
 using namespace std;

src/LinearAlgebra/LineSegmentSet.cpp

@@ -6 +6 @@
  */
 
-#include "LineSegmentSet.hpp"
+#include "LinearAlgebra/LineSegmentSet.hpp"
 
 #include "Helpers/Assert.hpp"
-#include "Line.hpp"
-#include "LineSegment.hpp"
+#include "LinearAlgebra/Line.hpp"
+#include "LinearAlgebra/LineSegment.hpp"
 
 #include "Helpers/Range.hpp"

src/LinearAlgebra/Matrix.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /*
  * Matrix.cpp
@@ -6 +13 @@
  */
 
-#include "Matrix.hpp"
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "Helpers/MemDebug.hpp"
+
+#include "LinearAlgebra/Matrix.hpp"
 #include "Helpers/Assert.hpp"
 #include "Exceptions/NotInvertibleException.hpp"
 #include "Helpers/fast_functions.hpp"
 #include "Helpers/Assert.hpp"
-#include "vector.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "VectorContent.hpp"
 #include "MatrixContent.hpp"
 
 #include <gsl/gsl_blas.h>
+#include <gsl/gsl_eigen.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_multimin.h>
+#include <gsl/gsl_vector.h>
 #include <cmath>
 #include <iostream>
@@ -96 +114 @@
 }
 
+void Matrix::zero(){
+  for(int i=NDIM;i--;){
+    for(int j=NDIM;j--;){
+      set(i,j,0.);
+    }
+  }
+}
+
+void Matrix::rotation(const double x, const double y, const double z)
+{
+  set(0,0, cos(y)*cos(z));
+  set(0,1, cos(z)*sin(x)*sin(y) - cos(x)*sin(z));
+  set(0,2, cos(x)*cos(z)*sin(y) + sin(x) * sin(z));
+  set(1,0, cos(y)*sin(z));
+  set(1,1, cos(x)*cos(z) + sin(x)*sin(y)*sin(z));
+  set(1,2, -cos(z)*sin(x) + cos(x)*sin(y)*sin(z));
+  set(2,0, -sin(y));
+  set(2,1, cos(y)*sin(x));
+  set(2,2, cos(x)*cos(y));
+}
+
 Matrix &Matrix::operator=(const Matrix &src){
   if(&src!=this){
@@ -103 +142 @@
 }
 
-Matrix &Matrix::operator+=(const Matrix &rhs){
+const Matrix &Matrix::operator+=(const Matrix &rhs){
   gsl_matrix_add(content->content, rhs.content->content);
   return *this;
 }
 
-Matrix &Matrix::operator-=(const Matrix &rhs){
+const Matrix &Matrix::operator-=(const Matrix &rhs){
   gsl_matrix_sub(content->content, rhs.content->content);
   return *this;
 }
 
-Matrix &Matrix::operator*=(const Matrix &rhs){
+const Matrix &Matrix::operator*=(const Matrix &rhs){
   (*this) = (*this)*rhs;
   return *this;
 }
 
-Matrix Matrix::operator+(const Matrix &rhs) const{
+const Matrix Matrix::operator+(const Matrix &rhs) const{
   Matrix tmp = *this;
   tmp+=rhs;
@@ -124 +163 @@
 }
 
-Matrix Matrix::operator-(const Matrix &rhs) const{
+const Matrix Matrix::operator-(const Matrix &rhs) const{
   Matrix tmp = *this;
   tmp-=rhs;
@@ -130 +169 @@
 }
 
-Matrix Matrix::operator*(const Matrix &rhs) const{
+const Matrix Matrix::operator*(const Matrix &rhs) const{
   gsl_matrix *res = gsl_matrix_alloc(NDIM, NDIM);
   gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, content->content, rhs.content->content, 0.0, res);
@@ -192 +231 @@
        - at(2,2)*at(1,0)*at(0,1);
 }
+
 
 Matrix Matrix::invert() const{
@@ -215 +255 @@
 Matrix Matrix::transpose() const{
   MatrixContent *newContent = new MatrixContent();
+  newContent->content = gsl_matrix_alloc(NDIM, NDIM);
   gsl_matrix_transpose_memcpy(newContent->content, content->content);
   Matrix res = Matrix(newContent);
@@ -220 +261 @@
 }
 
-Matrix &Matrix::operator*=(const double factor){
+Matrix &Matrix::transpose()
+{
+  double tmp;
+  for (int i=0;i<NDIM;i++)
+    for (int j=i+1;j<NDIM;j++) {
+      tmp = at(j,i);
+      at(j,i) = at(i,j);
+      at(i,j) = tmp;
+    }
+  return *this;
+}
+
+
+Vector Matrix::transformToEigenbasis()
+{
+  gsl_eigen_symmv_workspace *T = gsl_eigen_symmv_alloc(NDIM);
+  gsl_vector *eval = gsl_vector_alloc(NDIM);
+  gsl_matrix *evec = gsl_matrix_alloc(NDIM, NDIM);
+  gsl_eigen_symmv(content->content, eval, evec, T);
+  gsl_eigen_symmv_free(T);
+  gsl_matrix_memcpy(content->content, evec);
+  gsl_matrix_free(evec);
+  Vector evalues(gsl_vector_get(eval,0), gsl_vector_get(eval,1), gsl_vector_get(eval,2));
+  gsl_vector_free(eval);
+  return evalues;
+}
+
+const Matrix &Matrix::operator*=(const double factor){
   gsl_matrix_scale(content->content, factor);
   return *this;
 }
 
-Matrix operator*(const double factor,const Matrix& mat){
+const Matrix operator*(const double factor,const Matrix& mat){
   Matrix tmp = mat;
   tmp*=factor;
@@ -231 +299 @@
 }
 
-Matrix operator*(const Matrix &mat,const double factor){
+const Matrix operator*(const Matrix &mat,const double factor){
   return factor*mat;
 }
@@ -278 +346 @@
 
 Vector operator*(const Matrix &mat,const Vector &vec){
-  gsl_vector *res = gsl_vector_calloc(NDIM);
-  gsl_blas_dgemv( CblasNoTrans, 1.0, mat.content->content, vec.content->content, 0.0, res);
-  VectorContent *content = new VectorContent();
-  content->content = res;
-  return Vector(content);
+  Vector res;
+  gsl_blas_dgemv( CblasNoTrans, 1.0, mat.content->content, vec.content->content, 0.0, res.content->content);
+  return res;
 }
 

src/LinearAlgebra/Matrix.hpp

@@ -51 +51 @@
 
   /**
+   * Set all matrix entries to zero.
+   */
+  void zero();
+
+  /**
+   * Sets all matrix corresponding to a rotation matrix,
+   * first around the x-, then the y-, finally the z-axis
+   * with given angles.
+   */
+  void rotation(const double x, const double y, const double z);
+
+  /**
    * Access the matrix at index (i,j)
    */
@@ -96 +108 @@
   Matrix invert() const;
 
+  /**
+   * Diagonalizes a matrix and sets its rows to the resulting eigenvalues.
+   * The eigenvalues are returned as a vector.
+   *
+   * Rather costly, so use precomputation as often as possible.
+   */
+  Vector transformToEigenbasis();
+
+  /**
+   * Calculate the transpose of the matrix.
+   */
   Matrix transpose() const;
+  Matrix &transpose();
 
   // operators
   Matrix &operator=(const Matrix&);
 
-  Matrix &operator+=(const Matrix&);
-  Matrix &operator-=(const Matrix&);
-  Matrix &operator*=(const Matrix&);
+  const Matrix &operator+=(const Matrix&);
+  const Matrix &operator-=(const Matrix&);
+  const Matrix &operator*=(const Matrix&);
 
-  Matrix &operator*=(const double);
+  const Matrix &operator*=(const double);
 
-  Matrix operator+(const Matrix&) const;
-  Matrix operator-(const Matrix&) const;
-  Matrix operator*(const Matrix&) const;
+  const Matrix operator+(const Matrix&) const;
+  const Matrix operator-(const Matrix&) const;
+  const Matrix operator*(const Matrix&) const;
 
   bool operator==(const Matrix&) const;
@@ -123 +147 @@
 };
 
-Matrix operator*(const double,const Matrix&);
-Matrix operator*(const Matrix&,const double);
+const Matrix operator*(const double,const Matrix&);
+const Matrix operator*(const Matrix&,const double);
 
 /**

src/LinearAlgebra/Plane.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /*
  * Plane.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
-#include "Plane.hpp"
-#include "vector.hpp"
+#include "LinearAlgebra/Plane.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "defs.hpp"
-#include "info.hpp"
-#include "log.hpp"
-#include "verbose.hpp"
+#include "Helpers/Info.hpp"
+#include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "Helpers/Assert.hpp"
-#include "helpers.hpp"
+#include "Helpers/helpers.hpp"
 #include <cmath>
-#include "Line.hpp"
+#include "LinearAlgebra/Line.hpp"
 #include "Exceptions/MultipleSolutionsException.hpp"
 

src/LinearAlgebra/Plane.hpp

@@ -12 +12 @@
 #include <vector>
 #include <iosfwd>
-#include "Space.hpp"
+#include "LinearAlgebra/Space.hpp"
 #include "Exceptions/LinearDependenceException.hpp"
 #include "Exceptions/ZeroVectorException.hpp"

src/LinearAlgebra/Space.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /*
  * Space.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
-#include "Space.hpp"
-#include "vector.hpp"
+#include "LinearAlgebra/Space.hpp"
+#include "LinearAlgebra/Vector.hpp"
 
 Space::Space()

src/LinearAlgebra/Vector.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /** \file vector.cpp
  *
@@ -5 +12 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
-#include "vector.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "VectorContent.hpp"
-#include "verbose.hpp"
+#include "Helpers/Verbose.hpp"
 #include "World.hpp"
 #include "Helpers/Assert.hpp"
@@ -17 +29 @@
 #include <iostream>
 #include <gsl/gsl_blas.h>
+#include <gsl/gsl_vector.h>
 
 
@@ -51 +64 @@
 };
 
+/** Constructor of class vector.
+ */
+Vector::Vector(const double x[3])
+{
+  content = new VectorContent();
+  gsl_vector_set(content->content,0,x[0]);
+  gsl_vector_set(content->content,1,x[1]);
+  gsl_vector_set(content->content,2,x[2]);
+};
+
 Vector::Vector(VectorContent *_content) :
   content(_content)
@@ -92 +115 @@
   return (sqrt(DistanceSquared(y)));
 };
+
+size_t Vector::GreatestComponent() const
+{
+  int greatest = 0;
+  for (int i=1;i<NDIM;i++) {
+    if (at(i) > at(greatest))
+      greatest = i;
+  }
+  return greatest;
+}
+
+size_t Vector::SmallestComponent() const
+{
+  int smallest = 0;
+  for (int i=1;i<NDIM;i++) {
+    if (at(i) < at(smallest))
+      smallest = i;
+  }
+  return smallest;
+}
+
 
 Vector Vector::getClosestPoint(const Vector &point) const{

src/LinearAlgebra/Vector.hpp

@@ -17 +17 @@
 
 #include "defs.hpp"
-#include "Space.hpp"
+#include "LinearAlgebra/Space.hpp"
 
 /********************************************** declarations *******************************/
@@ -36 +36 @@
   Vector();
   Vector(const double x1, const double x2, const double x3);
+  Vector(const double x[3]);
   Vector(const Vector& src);
   virtual ~Vector();
@@ -63 +64 @@
   std::pair<Vector,Vector> partition(const Vector&) const;
   std::pair<pointset,Vector> partition(const pointset&) const;
+  size_t GreatestComponent() const;
+  size_t SmallestComponent() const;
 
   // Accessors ussually come in pairs... and sometimes even more than that

src/LinearAlgebra/VectorContent.hpp

@@ -14 +14 @@
  * Because of this the pointer to the gsl_vector struct is wrapped inside another
  * (dumb) object that allows for forward definitions.
+ *
+ * DO NOT USE OUTSIDE OF VECTOR UNLESS YOU ABSOLUTELY HAVE TO AND KNOW WHAT YOU ARE DOING.
  */
 

src/LinearAlgebra/VectorSet.hpp

@@ -20 +20 @@
  */
 
-#include "vector.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include <list>
 

src/LinearAlgebra/gslmatrix.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /*
  * gslmatrix.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
 using namespace std;
 
-#include "gslmatrix.hpp"
-#include "helpers.hpp"
+#include "LinearAlgebra/gslmatrix.hpp"
+#include "Helpers/helpers.hpp"
 #include "Helpers/fast_functions.hpp"
 

src/LinearAlgebra/gslvector.cpp

@@ +1 @@
+/*
+ * 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
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
@@ -12 +24 @@
 #include <iostream>
 
-#include "gslvector.hpp"
+#include "LinearAlgebra/gslvector.hpp"
 #include "defs.hpp"
-#include "vector.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "VectorContent.hpp"
 

src/LinearAlgebra/linearsystemofequations.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /*
  * linearsystemofequations.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
 #include "defs.hpp"
-#include "gslmatrix.hpp"
-#include "gslvector.hpp"
-#include "linearsystemofequations.hpp"
-#include "logger.hpp"
-#include "vector.hpp"
+#include "LinearAlgebra/gslmatrix.hpp"
+#include "LinearAlgebra/gslvector.hpp"
+#include "LinearAlgebra/linearsystemofequations.hpp"
+#include "Helpers/logger.hpp"
+#include "LinearAlgebra/Vector.hpp"
 
 #include <cassert>

src/LinearAlgebra/linearsystemofequations.hpp

@@ -6 +6 @@
  */
 
-using namespace std;
+#ifndef LINEARSYSTEMSOFEQUATIONS_HPP
+#define LINEARSYSTEMSOFEQUATIONS_HPP
 
 /*********************************************** includes ***********************************/
@@ -55 +56 @@
   bool IsSymmetric;
 };
+
+#endif /* LINEARSYSTEMSOFEQUATIONS_HPP */

src/LinearAlgebra/vector_ops.cpp

@@ +1 @@
+/*
+ * 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.
+ */
+
 /*
  * vector_ops.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
-#include "vector.hpp"
-#include "Plane.hpp"
-#include "log.hpp"
-#include "verbose.hpp"
-#include "gslmatrix.hpp"
+#include "LinearAlgebra/Vector.hpp"
+#include "LinearAlgebra/Plane.hpp"
+#include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
+#include "LinearAlgebra/gslmatrix.hpp"
 #include "leastsquaremin.hpp"
-#include "info.hpp"
+#include "Helpers/Info.hpp"
 #include "Helpers/fast_functions.hpp"
 #include "Exceptions/LinearDependenceException.hpp"