Changeset 0d4424 for src/LinearAlgebra

Timestamp:

Dec 4, 2010, 11:54:32 PM (14 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:

c134d9

Parents:

cca9ef

git-author:

Frederik Heber <heber@…> (11/15/10 14:02:38)

git-committer:

Frederik Heber <heber@…> (12/04/10 23:54:32)

Message:

Made gslmatrix obsolete.

• Transfered property and swap...() functions from GSLMatrix to MatrixContent.
• Line::getIntersection() uses now MatrixContent.
• made unit tests for gslmatrix into unit test for MatrixContent.

Location:

src/LinearAlgebra

Files:

• Line.cpp (modified) (2 diffs)
• MatrixContent.cpp (modified) (7 diffs)
• MatrixContent.hpp (modified) (4 diffs)
• linearsystemofequations.cpp (modified) (4 diffs)
• linearsystemofequations.hpp (modified) (2 diffs)

src/LinearAlgebra/Line.cpp

@@ -28 +28 @@
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
-#include "LinearAlgebra/gslmatrix.hpp"
+#include "LinearAlgebra/MatrixContent.hpp"
 #include "Helpers/Info.hpp"
 #include "Exceptions/LinearDependenceException.hpp"
@@ -116 +116 @@
   Vector res;
 
-  auto_ptr<GSLMatrix> M = auto_ptr<GSLMatrix>(new GSLMatrix(4,4));
-
-  M->SetAll(1.);
+  auto_ptr<MatrixContent> M = auto_ptr<MatrixContent>(new MatrixContent(4,4));
+
+  M->setValue(1.);
   for (int i=0;i<3;i++) {
-    M->Set(0, i, Line1a[i]);
-    M->Set(1, i, Line1b[i]);
-    M->Set(2, i, Line2a[i]);
-    M->Set(3, i, Line2b[i]);
+    M->set(0, i, Line1a[i]);
+    M->set(1, i, Line1b[i]);
+    M->set(2, i, Line2a[i]);
+    M->set(3, i, Line2b[i]);
   }
 

src/LinearAlgebra/MatrixContent.cpp

@@ -25 +25 @@
 #include <gsl/gsl_blas.h>
 #include <gsl/gsl_eigen.h>
+#include <gsl/gsl_linalg.h>
 #include <gsl/gsl_matrix.h>
 #include <gsl/gsl_multimin.h>
@@ -131 +132 @@
     for(int j=columns;j--;){
       set(i,j,0.);
+    }
+  }
+}
+
+/** Set all matrix components to a given value.
+ * \param _value value to set each component to
+ */
+void MatrixContent::setValue(double _value)
+{
+  for(int i=rows;i--;){
+    for(int j=columns;j--;){
+      set(i,j,_value);
     }
   }
@@ -196 +209 @@
 }
 
+/* ========================== Accessing =============================== */
+
 /** Accessor for manipulating component (i,j).
  * \param i row number
@@ -224 +239 @@
 }
 
+/** These functions return a pointer to the \a m-th element of a matrix.
+ *  If \a m or \a n lies outside the allowed range of 0 to GSLMatrix::dimension-1 then the error handler is invoked and a null pointer is returned.
+ * \param m index
+ * \return pointer to \a m-th element
+ */
+double *MatrixContent::Pointer(size_t m, size_t n)
+{
+  return gsl_matrix_ptr (content, m, n);
+};
+
+/** These functions return a constant pointer to the \a m-th element of a matrix.
+ *  If \a m or \a n lies outside the allowed range of 0 to GSLMatrix::dimension-1 then the error handler is invoked and a null pointer is returned.
+ * \param m index
+ * \return const pointer to \a m-th element
+ */
+const double *MatrixContent::const_Pointer(size_t m, size_t n) const
+{
+  return gsl_matrix_const_ptr (content, m, n);
+};
+
+/* ========================== Initializing =============================== */
+
 /** Setter for component (i,j).
  * \param i row numbr
@@ -238 +275 @@
 }
 
+/** This function sets the matrix from a double array.
+ * Creates a matrix view of the array and performs a memcopy.
+ * \param *x array of values (no dimension check is performed)
+ */
+void MatrixContent::setFromDoubleArray(double * x)
+{
+  gsl_matrix_view m = gsl_matrix_view_array (x, rows, columns);
+  gsl_matrix_memcpy (content, &m.matrix);
+};
+
+/* ====================== Exchanging elements ============================ */
+/** This function exchanges the \a i-th and \a j-th row of the matrix in-place.
+ * \param i i-th row to swap with ...
+ * \param j ... j-th row to swap against
+ */
+bool MatrixContent::SwapRows(size_t i, size_t j)
+{
+  return (gsl_matrix_swap_rows (content, i, j) == GSL_SUCCESS);
+};
+
+/** This function exchanges the \a i-th and \a j-th column of the matrix in-place.
+ * \param i i-th column to swap with ...
+ * \param j ... j-th column to swap against
+ */
+bool MatrixContent::SwapColumns(size_t i, size_t j)
+{
+  return (gsl_matrix_swap_columns (content, i, j) == GSL_SUCCESS);
+};
+
+/** This function exchanges the \a i-th row and \a j-th column of the matrix in-place.
+ * The matrix must be square for this operation to be possible.
+ * \param i i-th row to swap with ...
+ * \param j ... j-th column to swap against
+ */
+bool MatrixContent::SwapRowColumn(size_t i, size_t j)
+{
+  assert (rows == columns && "The matrix must be square for swapping row against column to be possible.");
+  return (gsl_matrix_swap_rowcol (content, i, j) == GSL_SUCCESS);
+};
+
 /** Return transposed matrix.
  * \return new matrix that is transposed of this.
@@ -244 +321 @@
 {
   std::cout << "const MatrixContent::transpose()." << std::endl;
-  gsl_matrix *res = gsl_matrix_alloc(rows, columns);
+  gsl_matrix *res = gsl_matrix_alloc(columns, rows);  // column and row dimensions exchanged!
   gsl_matrix_transpose_memcpy(res, content);
   MatrixContent newContent(res);
@@ -286 +363 @@
   return eval;
 }
+
+/* ============================ Properties ============================== */
+/** Checks whether matrix' elements are strictly null.
+ * \return true - is null, false - else
+ */
+bool MatrixContent::IsNull() const
+{
+  return gsl_matrix_isnull (content);
+};
+
+/** Checks whether matrix' elements are strictly positive.
+ * \return true - is positive, false - else
+ */
+bool MatrixContent::IsPositive() const
+{
+  return gsl_matrix_ispos (content);
+};
+
+/** Checks whether matrix' elements are strictly negative.
+ * \return true - is negative, false - else
+ */
+bool MatrixContent::IsNegative() const
+{
+  return gsl_matrix_isneg (content);
+};
+
+/** Checks whether matrix' elements are strictly non-negative.
+ * \return true - is non-negative, false - else
+ */
+bool MatrixContent::IsNonNegative() const
+{
+  return gsl_matrix_isnonneg (content);
+};
+
+/** This function performs a Cholesky decomposition to determine whether matrix is positive definite.
+ * We check whether GSL returns GSL_EDOM as error, indicating that decomposition failed due to matrix not being positive-definite.
+ * \return true - matrix is positive-definite, false - else
+ */
+bool MatrixContent::IsPositiveDefinite() const
+{
+  if (rows != columns)  // only possible for square matrices.
+    return false;
+  else
+    return (gsl_linalg_cholesky_decomp (content) != GSL_EDOM);
+};
+
+
+/** Calculates the determinant of the matrix.
+ * if matrix is square, uses LU decomposition.
+ */
+double MatrixContent::Determinant() const
+{
+  int signum = 0;
+  assert (rows == columns && "Determinant can only be calculated for square matrices.");
+  gsl_permutation *p = gsl_permutation_alloc(rows);
+  gsl_linalg_LU_decomp(content, p, &signum);
+  gsl_permutation_free(p);
+  return gsl_linalg_LU_det(content, signum);
+};
+
+/* ============================= Operators =============================== */
 
 /** Scalar multiplication operator.

src/LinearAlgebra/MatrixContent.hpp

@@ -41 +41 @@
   friend Vector operator*(const MatrixContent &mat,const Vector &vec);
   friend class RealSpaceMatrix;
+  friend class LinearSystemOfEquations;
+
+  friend class MatrixContentTest;
+  friend class MatrixContentSymmetricTest;
 public:
   MatrixContent(size_t rows, size_t columns);
@@ -53 +57 @@
   const double at(size_t i, size_t j) const;
   void set(size_t i, size_t j, const double value);
+  void setFromDoubleArray(double * x);
+
+  // Exchanging elements
+  bool SwapRows(size_t i, size_t j);
+  bool SwapColumns(size_t i, size_t j);
+  bool SwapRowColumn(size_t i, size_t j);
 
   // Transformations
@@ -59 +69 @@
   gsl_vector* transformToEigenbasis();
 
+  // Properties
+  bool IsNull() const;
+  bool IsPositive() const;
+  bool IsNegative() const;
+  bool IsNonNegative() const;
+  bool IsPositiveDefinite() const;
+  double Determinant() const;
+
   // Initializing
   void setIdentity();
   void setZero();
+  void setValue(double _value);
 
   // Operators
@@ -72 +91 @@
   bool operator==(const MatrixContent &rhs) const;
 
+protected:
+  double *Pointer(size_t m, size_t n);
+  const double *const_Pointer(size_t m, size_t n) const;
 
 private:

src/LinearAlgebra/linearsystemofequations.cpp

@@ -21 +21 @@
 
 #include "defs.hpp"
-#include "LinearAlgebra/gslmatrix.hpp"
+#include "LinearAlgebra/MatrixContent.hpp"
 #include "LinearAlgebra/gslvector.hpp"
 #include "LinearAlgebra/linearsystemofequations.hpp"
@@ -37 +37 @@
 LinearSystemOfEquations::LinearSystemOfEquations(int m, int n) : rows(m), columns(n), IsSymmetric(false)
 {
-  A = new GSLMatrix(m, n);
+  A = new MatrixContent(m, n);
   b = new GSLVector(m);
   x = new GSLVector(n);
@@ -85 +85 @@
 void LinearSystemOfEquations::SetA(double *x)
 {
-  A->SetFromDoubleArray(x);
+  A->setFromDoubleArray(x);
 };
 
@@ -129 +129 @@
   if (IsSymmetric) { // use LU
     gsl_permutation * p = gsl_permutation_alloc (x->dimension);
-    gsl_linalg_LU_decomp (A->matrix, p, &s);
-    gsl_linalg_LU_solve (A->matrix, p, b->vector, x->vector);
+    gsl_linalg_LU_decomp (A->content, p, &s);
+    gsl_linalg_LU_solve (A->content, p, b->vector, x->vector);
     gsl_permutation_free (p);
   } else {  // use Householder
-    //GSLMatrix *backup = new GSLMatrix(rows,columns);
+    //MatrixContent *backup = new MatrixContent(rows,columns);
     //*backup = *A;
-    gsl_linalg_HH_solve (A->matrix, b->vector, x->vector);
+    gsl_linalg_HH_solve (A->content, b->vector, x->vector);
     //*A = *backup;
     //delete(backup);

src/LinearAlgebra/linearsystemofequations.hpp

@@ -21 +21 @@
 
 class Vector;
-class GSLMatrix;
+class MatrixContent;
 class GSLVector;
 
@@ -46 +46 @@
   GSLVector *b;
   GSLVector *x;
-  GSLMatrix *A;
+  MatrixContent *A;
 
 private: