Changeset f03705 for src/LinearAlgebra/MatrixContent.cpp

Timestamp:

Dec 5, 2010, 12:19:33 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, Candidate_v1.7.0, 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:

001f8a

Parents:

6e06bd (diff), e828c0 (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.

Message:

Merge branch 'SubspaceFactorizer' into stable

File:

• src/LinearAlgebra/MatrixContent.cpp (modified) (16 diffs)

src/LinearAlgebra/MatrixContent.cpp

@@ -15 +15 @@
 
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
+#include "Exceptions/NotInvertibleException.hpp"
 #include "Helpers/Assert.hpp"
-#include "Exceptions/NotInvertibleException.hpp"
+#include "Helpers/defs.hpp"
 #include "Helpers/fast_functions.hpp"
-#include "Helpers/Assert.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "LinearAlgebra/VectorContent.hpp"
@@ -30 +30 @@
 #include <gsl/gsl_vector.h>
 #include <cmath>
+#include <cassert>
 #include <iostream>
+#include <set>
 
 using namespace std;
@@ -45 +47 @@
   content = gsl_matrix_calloc(rows, columns);
 }
+
+/** Constructor of class VectorContent.
+ * We need this MatrixBaseCase for the VectorContentView class.
+ * There no content should be allocated, as it is just a view with an internal
+ * gsl_vector_view. Hence, MatrixBaseCase is just dummy class to give the
+ * constructor a unique signature.
+ * \param MatrixBaseCase
+ */
+MatrixContent::MatrixContent(size_t _rows, size_t _columns, MatrixBaseCase) :
+    rows(_rows),
+    columns(_columns)
+{}
 
 /** Constructor for class MatrixContent.
@@ -52 +66 @@
  */
 MatrixContent::MatrixContent(size_t _rows, size_t _columns, const double *src) :
-        rows(_rows),
-        columns(_columns)
+    rows(_rows),
+    columns(_columns)
 {
   content = gsl_matrix_calloc(rows, columns);
@@ -75 +89 @@
  */
 MatrixContent::MatrixContent(gsl_matrix *&src) :
-        rows(src->size1),
-        columns(src->size2)
+    rows(src->size1),
+    columns(src->size2)
 {
   content = gsl_matrix_alloc(src->size1, src->size2);
@@ -88 +102 @@
  */
 MatrixContent::MatrixContent(const MatrixContent &src) :
-        rows(src.rows),
-        columns(src.columns)
+    rows(src.rows),
+    columns(src.columns)
 {
   content = gsl_matrix_alloc(src.rows, src.columns);
@@ -99 +113 @@
  */
 MatrixContent::MatrixContent(const MatrixContent *src) :
-        rows(src->rows),
-        columns(src->columns)
+    rows(src->rows),
+    columns(src->columns)
 {
   ASSERT(src != NULL, "MatrixContent::MatrixContent - pointer to source matrix is NULL!");
@@ -114 +128 @@
 }
 
+/** Getter for MatrixContent::rows.
+ * \return MatrixContent::rows
+ */
+const size_t MatrixContent::getRows() const
+{
+  return rows;
+}
+
+/** Getter for MatrixContent::columns.
+ * \return MatrixContent::columns
+ */
+const size_t MatrixContent::getColumns() const
+{
+  return columns;
+}
+
+/** Return a VectorViewContent of the \a column -th column vector.
+ *
+ * @param column index of column
+ * @return column of matrix as VectorContent
+ */
+VectorContent *MatrixContent::getColumnVector(size_t column) const
+{
+  ASSERT(column < columns,
+      "MatrixContent::getColumnVector() - requested column "+toString(column)
+      +" greater than dimension "+toString(columns));
+  return (new VectorViewContent(gsl_matrix_column(content,column)));
+}
+
+/** Returns a VectorViewContent of the \a row -th row vector.
+ * @param row row index
+ * @return VectorContent of row vector
+ */
+VectorContent *MatrixContent::getRowVector(size_t row) const
+{
+  ASSERT(row < rows,
+      "MatrixContent::getColumnVector() - requested row "+toString(row)
+      +" greater than dimension "+toString(rows));
+  return (new VectorViewContent(gsl_matrix_row(content,row)));
+}
+
+/** Returns the main diagonal of the matrix as VectorContent.
+ * @return diagonal as VectorContent.
+ */
+VectorContent *MatrixContent::getDiagonalVector() const
+{
+  return (new VectorViewContent(gsl_matrix_diagonal(content)));
+}
+
 /** Set matrix to identity.
  */
@@ -120 +183 @@
   for(int i=rows;i--;){
     for(int j=columns;j--;){
-      set(i,j,i==j);
+      set(i,j,(double)(i==j));
     }
   }
@@ -187 +250 @@
 const MatrixContent &MatrixContent::operator*=(const MatrixContent &rhs)
 {
-  ASSERT(rows == rhs.rows,
-      "MatrixContent::operator*=() - row dimension differ: "+toString(rows)+" != "+toString(rhs.rows)+".");
-  ASSERT(columns == rhs.columns,
-      "MatrixContent::operator*=() - columns dimension differ: "+toString(columns)+" != "+toString(rhs.columns)+".");
+  ASSERT(rhs.columns == rhs.rows,
+      "MatrixContent::operator*=() - rhs matrix is not square: "+toString(rhs.columns)+" != "+toString(rhs.rows)+".");
+  ASSERT(columns == rhs.rows,
+      "MatrixContent::operator*=() - columns dimension differ: "+toString(columns)+" != "+toString(rhs.rows)+".");
   (*this) = (*this)*rhs;
   return *this;
@@ -201 +264 @@
 const MatrixContent MatrixContent::operator*(const MatrixContent &rhs) const
 {
-  gsl_matrix *res = gsl_matrix_alloc(rows, columns);
+  ASSERT (columns == rhs.rows,
+      "MatrixContent::operator*() - dimensions not match for matrix product (a,b)*(b,c) = (a,c):"
+      "("+toString(rows)+","+toString(columns)+")*("+toString(rhs.rows)+","+toString(rhs.columns)+")");
+  gsl_matrix *res = gsl_matrix_alloc(rows, rhs.columns);
   gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, content, rhs.content, 0.0, res);
   // gsl_matrix is taken over by constructor, hence no free
@@ -209 +275 @@
 }
 
+/** Hadamard multiplication with copy operator.
+ * The Hadamard product is component-wise matrix product.
+ * \param &rhs matrix to hadamard-multiply with
+ * \return reference to newly allocated MatrixContent
+ */
+const MatrixContent MatrixContent::operator&(const MatrixContent &rhs) const
+{
+  ASSERT ((rows == rhs.rows) && (columns == rhs.columns),
+      "MatrixContent::operator&() - dimensions not match for matrix product (a,b) != (b,c):"
+      "("+toString(rows)+","+toString(columns)+") != ("+toString(rhs.rows)+","+toString(rhs.columns)+")");
+  gsl_matrix *res = gsl_matrix_alloc(rows, rhs.columns);
+  for (size_t i=0;i<rows;++i)
+    for (size_t j=0;j<columns;++j)
+      gsl_matrix_set(res, i,j, gsl_matrix_get(content, i,j)*gsl_matrix_get(rhs.content, i,j));
+  // gsl_matrix is taken over by constructor, hence no free
+  MatrixContent tmp(res);
+  gsl_matrix_free(res);
+  return tmp;
+}
+
+/** Hadamard multiplication with copy operator.
+ * The Hadamard product is component-wise matrix product.
+ * Note that Hadamard product can easily be done on top of \a *this matrix.
+ * Hence, we don't need to use the multiply and copy operator as in the case of
+ * MatrixContent::operator*=().
+ * \param &rhs matrix to hadamard-multiply with
+ * \return reference to newly allocated MatrixContent
+ */
+const MatrixContent &MatrixContent::operator&=(const MatrixContent &rhs)
+{
+  ASSERT ((rows == rhs.rows) && (columns == rhs.columns),
+      "MatrixContent::operator&() - dimensions not match for matrix product (a,b) != (b,c):"
+      "("+toString(rows)+","+toString(columns)+") != ("+toString(rhs.rows)+","+toString(rhs.columns)+")");
+  for (size_t i=0;i<rows;++i)
+    for (size_t j=0;j<columns;++j)
+      gsl_matrix_set(content, i,j, gsl_matrix_get(content, i,j)*gsl_matrix_get(rhs.content, i,j));
+  return *this;
+}
+
 /* ========================== Accessing =============================== */
 
@@ -311 +416 @@
 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.");
+  ASSERT (rows == columns,
+      "MatrixContent::SwapRowColumn() - The matrix must be square for swapping row against column to be possible.");
   return (gsl_matrix_swap_rowcol (content, i, j) == GSL_SUCCESS);
 };
@@ -344 +450 @@
 }
 
-/** Transform the matrix to its eigenbasis ans return resulting eigenvalues.
+/** Transform the matrix to its eigenbasis and return resulting eigenvalues.
+ * Note that we only return real-space part in case of non-symmetric matrix.
  * \warn return vector has to be freed'd
+ * TODO: encapsulate return value in boost::shared_ptr or in VectorContent.
  * \return gsl_vector pointer to vector of eigenvalues
  */
 gsl_vector* MatrixContent::transformToEigenbasis()
 {
-  ASSERT (rows == columns,
-      "MatrixContent::transformToEigenbasis() - only implemented for square matrices: "+toString(rows)+"!="+toString(columns)+"!");
-  gsl_eigen_symmv_workspace *T = gsl_eigen_symmv_alloc(rows);
-  gsl_vector *eval = gsl_vector_alloc(rows);
-  gsl_matrix *evec = gsl_matrix_alloc(rows, rows);
-  gsl_eigen_symmv(content, eval, evec, T);
-  gsl_eigen_symmv_free(T);
-  gsl_matrix_memcpy(content, evec);
-  gsl_matrix_free(evec);
-  return eval;
+  if (rows == columns) { // symmetric
+    gsl_eigen_symmv_workspace *T = gsl_eigen_symmv_alloc(rows);
+    gsl_vector *eval = gsl_vector_alloc(rows);
+    gsl_matrix *evec = gsl_matrix_alloc(rows, rows);
+    gsl_eigen_symmv(content, eval, evec, T);
+    gsl_eigen_symmv_free(T);
+    gsl_matrix_memcpy(content, evec);
+    gsl_matrix_free(evec);
+    return eval;
+  } else { // non-symmetric
+    // blow up gsl_matrix in content to square matrix, fill other components with zero
+    const size_t greaterDimension = rows > columns ? rows : columns;
+    gsl_matrix *content_square = gsl_matrix_alloc(greaterDimension, greaterDimension);
+    for (size_t i=0; i<greaterDimension; i++) {
+      for (size_t j=0; j<greaterDimension; j++) {
+        const double value = ((i < rows) && (j < columns)) ? gsl_matrix_get(content,i,j) : 0.;
+        gsl_matrix_set(content_square, i,j, value);
+      }
+    }
+
+    // show squared matrix by putting it into a MatrixViewContent
+    MatrixContent *ContentSquare = new MatrixViewContent(gsl_matrix_submatrix(content_square,0,0,content_square->size1, content_square->size2));
+    std::cout << "The squared matrix is " << *ContentSquare << std::endl;
+
+    // solve eigenvalue problem
+    gsl_eigen_nonsymmv_workspace *T = gsl_eigen_nonsymmv_alloc(rows);
+    gsl_vector_complex *eval = gsl_vector_complex_alloc(greaterDimension);
+    gsl_matrix_complex *evec = gsl_matrix_complex_alloc(greaterDimension, greaterDimension);
+    gsl_eigen_nonsymmv(content_square, eval, evec, T);
+    gsl_eigen_nonsymmv_free(T);
+
+    // copy eigenvectors real-parts into content_square and ...
+    for (size_t i=0; i<greaterDimension; i++)
+      for (size_t j=0; j<greaterDimension; j++)
+        gsl_matrix_set(content_square, i,j, GSL_REAL(gsl_matrix_complex_get(evec,i,j)));
+
+    // ... show complex-valued eigenvector matrix
+    std::cout << "The real-value eigenvector matrix is " << *ContentSquare << std::endl;
+//    std::cout << "Resulting eigenvector matrix is [";
+//    for (size_t i=0; i<greaterDimension; i++) {
+//      for (size_t j=0; j<greaterDimension; j++) {
+//        std::cout << "(" << GSL_REAL(gsl_matrix_complex_get(evec,i,j))
+//            << "," << GSL_IMAG(gsl_matrix_complex_get(evec,i,j)) << ")";
+//        if (j < greaterDimension-1)
+//          std::cout << " ";
+//      }
+//      if (i < greaterDimension-1)
+//        std::cout << "; ";
+//    }
+//    std::cout << "]" << std::endl;
+
+    // copy real-parts of complex eigenvalues and eigenvectors (column-wise orientation)
+    gsl_vector *eval_real = gsl_vector_alloc(columns);
+    size_t I=0;
+    for (size_t i=0; i<greaterDimension; i++) { // only copy real space part
+      if (fabs(GSL_REAL(gsl_vector_complex_get(eval,i))) > MYEPSILON) { // only take eigenvectors with value > 0
+        std::cout << i << "th eigenvalue is (" << GSL_REAL(gsl_vector_complex_get(eval,i)) << "," << GSL_IMAG(gsl_vector_complex_get(eval,i)) << ")" << std::endl;
+        for (size_t j=0; j<greaterDimension; j++) {
+          if (fabs(GSL_IMAG(gsl_matrix_complex_get(evec,j,i))) > MYEPSILON)
+            std::cerr << "MatrixContent::transformToEigenbasis() - WARNING: eigenvectors are complex-valued!" << std::endl;
+          gsl_matrix_set(content, j,I, GSL_REAL(gsl_matrix_complex_get(evec,j,i)));
+        }
+        if (fabs(GSL_IMAG(gsl_vector_complex_get(eval,I))) > MYEPSILON)
+          std::cerr << "MatrixContent::transformToEigenbasis() - WARNING: eigenvectors are complex-valued!" << std::endl;
+        gsl_vector_set(eval_real, I, GSL_REAL(gsl_vector_complex_get(eval, i)));
+        I++;
+      }
+    }
+    gsl_matrix_complex_free(evec);
+    gsl_vector_complex_free(eval);
+    delete ContentSquare;
+
+    return eval_real;
+  }
+}
+
+
+/** Sorts the eigenpairs in ascending order of the eigenvalues.
+ * We assume that MatrixContent::transformToEigenbasis() has just been called.
+ * @param eigenvalues vector of eigenvalue from
+ *        MatrixContent::transformToEigenbasis()
+ */
+void MatrixContent::sortEigenbasis(gsl_vector *eigenvalues)
+{
+  gsl_eigen_symmv_sort (eigenvalues, content,
+                          GSL_EIGEN_SORT_ABS_ASC);
 }
 
@@ -414 +598 @@
 {
   int signum = 0;
-  assert (rows == columns && "Determinant can only be calculated for square matrices.");
+  ASSERT(rows == columns,
+      "MatrixContent::Determinant() - determinant can only be calculated for square matrices.");
   gsl_permutation *p = gsl_permutation_alloc(rows);
   gsl_linalg_LU_decomp(content, p, &signum);
@@ -473 +658 @@
 }
 
-Vector operator*(const MatrixContent &mat,const Vector &vec)
-{
-  Vector result;
-  gsl_blas_dgemv( CblasNoTrans, 1.0, mat.content, vec.content->content, 0.0, result.content->content);
-  return result;
-}
+
+std::ostream & operator<<(std::ostream &ost, const MatrixContent &mat)
+{
+  ost << "\\begin{pmatrix}";
+  for (size_t i=0;i<mat.rows;i++) {
+    for (size_t j=0;j<mat.columns;j++) {
+      ost << mat.at(i,j) << " ";
+      if (j != mat.columns-1)
+        ost << "& ";
+    }
+    if (i != mat.rows-1)
+      ost << "\\\\ ";
+  }
+  ost << "\\end{pmatrix}";
+  return ost;
+}