Changeset 17fa81 for src

Timestamp:

Dec 4, 2010, 11:56:27 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:

041462

Parents:

5eec98

git-author:

Frederik Heber <heber@…> (11/16/10 11:42:47)

git-committer:

Frederik Heber <heber@…> (12/04/10 23:56:27)

Message:

MatrixContent::transformToEigenbasis() also working for non-symmetric real matrices.

• we don't have to look for zero columns OR rows, as eigenvectors are stored column-wise and eigenvalues give clear identification of the right/non-zero ones.
• also added ASSERT to MatrixContent::operator*().

File:

• src/LinearAlgebra/MatrixContent.cpp (modified) (6 diffs)

src/LinearAlgebra/MatrixContent.cpp

@@ -215 +215 @@
 const MatrixContent MatrixContent::operator*(const MatrixContent &rhs) const
 {
+  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);
@@ -358 +361 @@
 }
 
-/** 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
@@ -376 +379 @@
     return eval;
   } else { // non-symmetric
-    //ASSERT(false, "MatrixContent::transformToEigenbasis() - only implemented for square matrices: "+toString(rows)+"!="+toString(columns)+"!");
-
     // blow up gsl_matrix in content to square matrix, fill other components with zero
     const size_t greaterDimension = rows > columns ? rows : columns;
@@ -388 +389 @@
     }
 
-    // show squared matrix
-    MatrixContent *ContentSquare = new MatrixViewContent(gsl_matrix_submatrix(content,0,0,content->size1, content->size2));
+    // 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;
-    delete ContentSquare;
 
     // solve eigenvalue problem
@@ -401 +401 @@
 
     // 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 << "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 << " ";
-        gsl_matrix_set(content_square, i,j, GSL_REAL(gsl_matrix_complex_get(evec,i,j)));
-      }
-      if (i < greaterDimension-1)
-        std::cout << "; ";
-    }
-    std::cout << "]" << std::endl;
-
-    // scan for zero rows and columns to drop
-    std::set<size_t> RowDropList;
-    std::set<size_t> ColumnDropList;
+    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
-      double Rsum = 0.;
-      double Csum = 0.;
-      for (size_t j=0; j<greaterDimension; j++) {
-        Rsum += fabs(GSL_REAL(gsl_matrix_complex_get(evec,i,j)));
-        Csum += fabs(GSL_REAL(gsl_matrix_complex_get(evec,j,i)));
-      }
-      Rsum /= (double)greaterDimension;
-      Csum /= (double)greaterDimension;
-      if (Rsum < MYEPSILON)
-        RowDropList.insert(i);
-      if (Csum < MYEPSILON)
-        ColumnDropList.insert(i);
-    }
-
-    // copy real-parts of complex eigenvalues and eigenvectors
-    gsl_vector *eval_real = gsl_vector_alloc(greaterDimension);
-    size_t I=0;
-    size_t J=0;
-    for (size_t i=0; i<greaterDimension; i++) { // only copy real space part
-      if (RowDropList.find(i) == RowDropList.end()) {
+      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 (ColumnDropList.find(j) == ColumnDropList.end()) {
-            if (fabs(GSL_IMAG(gsl_matrix_complex_get(evec,i,j))) > MYEPSILON)
-              std::cerr << "MatrixContent::transformToEigenbasis() - WARNING: eigenvectors are complex-valued!" << std::endl;
-            gsl_matrix_set(content, I,J, GSL_REAL(gsl_matrix_complex_get(evec,i,j)));
-            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)
@@ -456 +439 @@
     gsl_matrix_complex_free(evec);
     gsl_vector_complex_free(eval);
+    delete ContentSquare;
+
     return eval_real;
   }