Changeset e828c0 for src/LinearAlgebra/Subspace.cpp

Timestamp:

Dec 4, 2010, 11:56:28 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:

4fbca9c, f03705

Parents:

1fb318

git-author:

Frederik Heber <heber@…> (12/04/10 18:10:56)

git-committer:

Frederik Heber <heber@…> (12/04/10 23:56:28)

Message:

SubspaceFactorizer is now hierarchical.

• higher order subspace matrices are only corrections to lower order ones.
• i.e. eigenvectors obtained from there have all lower ones projected and substracted.

File:

• src/LinearAlgebra/Subspace.cpp (modified) (12 diffs)

src/LinearAlgebra/Subspace.cpp

@@ -49 +49 @@
 
   // create eigenspace matrices
-  projectFullSpaceMatrixToSubspace();
+  EigenspaceMatrix = projectFullspaceMatrixToSubspace(FullSpace.getEigenspaceMatrix());
 }
 
@@ -62 +62 @@
 /** Diagonalizes the subspace matrix.
  *
- * @param fullmatrix full matrix to project into subspace and solve
  */
 void Subspace::calculateEigenSubspace()
@@ -69 +68 @@
   createProjectionMatrices();
   // remove subsubspace directions
-  correctEigenvectorsFromSubIndices();
+  //correctProjectionMatricesFromSubIndices();
   // solve
-  projectFullSpaceMatrixToSubspace();
+  EigenspaceMatrix = projectFullspaceMatrixToSubspace(FullSpace.getEigenspaceMatrix());
   EigenvectorMatrix = EigenspaceMatrix;
   VectorContent *EigenvalueVector = new VectorContent(EigenvectorMatrix.transformToEigenbasis());
@@ -79 +78 @@
   }
   delete EigenvalueVector;
-  Log() << Verbose(2) << "Eigenvector matrix is " << EigenvectorMatrix << std::endl;
-  Log() << Verbose(2) << "Eigenvalues are " << Eigenvalues << std::endl;
+
   // create mapping
   createLocalMapping();
+
+  // swap the eigenvectors/-values to their correct sequence
+  sortEigenvectors();
+
+  // scale eigenvectors by their eigenvalues for the subsequent correction
+  scaleEigenvectorsbyEigenvalue();
+
+  // let only remain corrections to lower orders on this order
+  correctEigenvectorsFromSubIndices();
+
+  if (!EigenvectorMatrix.IsNull()) {
+    // get correct eigenvalues
+    getNormofEigenvectorAsEigenvalue();
+
+    DoLog(2) && (Log() << Verbose(2) << "Eigenvector matrix is " << EigenvectorMatrix << std::endl);
+    DoLog(2) && (Log() << Verbose(2) << "Eigenvalues are " << Eigenvalues << std::endl);
+
+  }
 }
 
@@ -123 +139 @@
 
 
+/** Sort the eigenvectors in the order of Subspace::Indices.
+ *
+ */
+void Subspace::sortEigenvectors()
+{
+  DoLog(1) && (Log() << Verbose(1) << "Sorting Eigenvectors ..." << std::endl);
+  MatrixContent tempMatrix = EigenvectorMatrix;
+  eigenvalueset tempValues = Eigenvalues;
+  size_t localindex = 0;
+  BOOST_FOREACH( size_t iter, Indices) {
+    Log() << Verbose(1) << GlobalToLocal[iter] << "th eigenvector is associated to "
+        << iter << " and goes to column " << localindex << "." << std::endl;
+    boost::shared_ptr<VectorContent> columnvector(tempMatrix.getColumnVector(GlobalToLocal[iter]));
+    *Eigenvectors[localindex] = *columnvector;
+    Eigenvalues[localindex] = tempValues[GlobalToLocal[iter]];
+    ++localindex;
+  }
+}
+
+
+/** We remove the projections from lower subspaces from our Eigenspacematrix.
+ * This is intended to diminish parallel changing of eigenspaces.
+ */
 void Subspace::correctEigenvectorsFromSubIndices()
 {
+  DoLog(1) && (Log() << Verbose(1) << "Correcting EigenvectorMatrix ... " << std::endl);
+  BOOST_FOREACH( boost::shared_ptr<Subspace> iter, SubIndices ) {
+    const MatrixContent tempMatrix =
+        projectFullspaceMatrixToSubspace(
+            iter->projectSubspaceMatrixToFullspace(iter->getEigenvectorMatrix())
+            );
+    DoLog(1) && (Log() << Verbose(1) << "Subtracting matrix from " << *iter << ":" << tempMatrix << std::endl);
+    EigenvectorMatrix -= tempMatrix;
+  }
+  DoLog(1) && (Log() << Verbose(1) << "Corrected EigenvectorMatrix is " << EigenvectorMatrix << std::endl);
+
+  // check for null vectors
+  const size_t max = EigenvectorMatrix.getColumns();
+  for(size_t i = 0; i< max; ++i) {
+    if (Eigenvectors[i]->IsZero()) {
+      Eigenvalues[i] = 0.;
+      Eigenvectors[i]->setZero();
+    }
+  }
+}
+
+
+/** Scale the local eigenvectors each by their eigenvalue.
+ *
+ */
+void Subspace::scaleEigenvectorsbyEigenvalue()
+{
+  size_t localindex = 0;
+  BOOST_FOREACH( boost::shared_ptr<VectorContent> ev, Eigenvectors) {
+    *ev *= Eigenvalues[localindex];
+    ++localindex;
+  }
+}
+
+
+/** Get Norm of each eigenvector to serve als eigenvalue.
+ *
+ */
+void Subspace::getNormofEigenvectorAsEigenvalue()
+{
+  size_t localindex = 0;
+  BOOST_FOREACH( boost::shared_ptr<VectorContent> ev, Eigenvectors) {
+    Eigenvalues[localindex] = ev->Norm();
+    ++localindex;
+  }
+}
+
+
+/** We remove the projections from lower subspaces from our Eigenspacematrix.
+ * This is intended to diminish parallel changing of eigenspaces.
+ */
+void Subspace::correctProjectionMatricesFromSubIndices()
+{
+  MatrixContent subtractMatrix(ProjectToSubspace.getRows(), ProjectToSubspace.getColumns());
+  DoLog(1) && (Log() << Verbose(1) << "Correcting ProjectToSubspace ... " << std::endl);
+  BOOST_FOREACH( boost::shared_ptr<Subspace> iter, SubIndices ) {
+    const MatrixContent tempMatrix = iter->getEigenvectorMatrix();
+    const MatrixContent tempMatrix2 = iter->projectSubspaceMatrixToFullspace(tempMatrix);
+    const MatrixContent tempMatrix3 = (tempMatrix2 * ProjectToSubspace);
+    DoLog(1) && (Log() << Verbose(1) << "Subtracting matrix from " << *iter << ":" << tempMatrix3 << std::endl);
+    subtractMatrix += tempMatrix3;
+  }
+  ProjectToSubspace -= subtractMatrix;
+  DoLog(1) && (Log() << Verbose(1) << "Corrected ProjectToSubspace is " << ProjectToSubspace << std::endl);
+
+  ProjectFromSubspace = ((const MatrixContent)ProjectToSubspace).transpose();
+  DoLog(1) && (Log() << Verbose(1) << "Corrected ProjectFromSubspace is " << ProjectFromSubspace << std::endl);
 }
 
@@ -198 +304 @@
 
 
+/** Getter for Subspace::SubIndices.
+ *
+ * @return const reference to Subspace::SubIndices.
+ */
+const Subspace::subset & Subspace::getSubIndices() const
+{
+  return SubIndices;
+}
+
 /** Remove a subset of indices from the SubIndices.
  *
@@ -236 +351 @@
 {
   // check whether bigmatrix is at least as big as EigenspaceMatrix
-  ASSERT(EigenspaceMatrix.getRows() <= Eigenvectors[0]->getDimension(),
+  ASSERT(EigenspaceMatrix.getRows() <= FullSpace.getEigenspaceMatrix().getRows(),
       "embedEigenspaceMatrix() - EigenspaceMatrix has more rows "
-      +toString(EigenspaceMatrix.getRows())+" than eigenvectors "
+      +toString(EigenspaceMatrix.getRows())+" than FullSpace::EigenspaceMatrix "
       +toString(Eigenvectors[0]->getDimension())+"!");
-  ASSERT(EigenspaceMatrix.getColumns() <= Eigenvectors.size(),
+  ASSERT(EigenspaceMatrix.getColumns() <= FullSpace.getEigenspaceMatrix().getColumns(),
       "embedEigenspaceMatrix() - EigenspaceMatrix has more columns "
-      +toString(EigenspaceMatrix.getColumns())+" than eigenvectors "
+      +toString(EigenspaceMatrix.getColumns())+" than FullSpace::EigenspaceMatrix "
       +toString(Eigenvectors.size())+"!");
   // check whether EigenspaceMatrix is big enough for both index sets
@@ -255 +370 @@
 
   // construct intermediate matrix
-  MatrixContent *intermediatematrix = new MatrixContent(Eigenvectors[0]->getDimension(), Indices.size());
-  size_t localcolumn = 0;
-  BOOST_FOREACH(size_t columnindex, Indices) {
-    // create two vectors from each row and copy assign them
-    boost::shared_ptr<VectorContent> srceigenvector(Eigenvectors[columnindex]);
-    boost::shared_ptr<VectorContent> desteigenvector(intermediatematrix->getColumnVector(localcolumn));
-    *desteigenvector = *srceigenvector;
-    localcolumn++;
-  }
-  // matrix product with eigenbasis EigenspaceMatrix matrix
-  *intermediatematrix *= EigenspaceMatrix;
-
-  // and place at right columns into bigmatrix
-  MatrixContent *bigmatrix = new MatrixContent(Eigenvectors[0]->getDimension(), Eigenvectors.size());
-  bigmatrix->setZero();
-  localcolumn = 0;
-  BOOST_FOREACH(size_t columnindex, Indices) {
-    // create two vectors from each row and copy assign them
-    boost::shared_ptr<VectorContent> srceigenvector(intermediatematrix->getColumnVector(localcolumn));
-    boost::shared_ptr<VectorContent> desteigenvector(bigmatrix->getColumnVector(columnindex));
-    *desteigenvector = *srceigenvector;
-    localcolumn++;
-  }
+  MatrixContent *bigmatrix = new MatrixContent(
+      FullSpace.getEigenspaceMatrix().getRows(),
+      FullSpace.getEigenspaceMatrix().getColumns());
+  *bigmatrix = ProjectToSubspace * EigenspaceMatrix * ProjectFromSubspace;
+
+//  MatrixContent *intermediatematrix = new MatrixContent(FullSpace.getEigenspaceMatrix().getRows(), Indices.size());
+//  size_t localcolumn = 0;
+//  BOOST_FOREACH(size_t columnindex, Indices) {
+//    // create two vectors from each row and copy assign them
+//    boost::shared_ptr<VectorContent> srceigenvector(Eigenvectors[columnindex]);
+//    boost::shared_ptr<VectorContent> desteigenvector(intermediatematrix->getColumnVector(localcolumn));
+//    *desteigenvector = *srceigenvector;
+//    localcolumn++;
+//  }
+//  // matrix product with eigenbasis EigenspaceMatrix matrix
+//  *intermediatematrix *= EigenspaceMatrix;
+//
+//  // and place at right columns into bigmatrix
+//  MatrixContent *bigmatrix = new MatrixContent(FullSpace.getEigenspaceMatrix().getRows(), Eigenvectors.size());
+//  bigmatrix->setZero();
+//  localcolumn = 0;
+//  BOOST_FOREACH(size_t columnindex, Indices) {
+//    // create two vectors from each row and copy assign them
+//    boost::shared_ptr<VectorContent> srceigenvector(intermediatematrix->getColumnVector(localcolumn));
+//    boost::shared_ptr<VectorContent> desteigenvector(bigmatrix->getColumnVector(columnindex));
+//    *desteigenvector = *srceigenvector;
+//    localcolumn++;
+//  }
 
   return *bigmatrix;
@@ -302 +422 @@
   BOOST_FOREACH(size_t iter, Indices) {
     *ColumnVectors[localindex] = FullSpace.getEigenvector(iter);
-    localindex++;
-  }
-  Log() << Verbose(2) << "ProjectionToSubspace matrix is " << ProjectToSubspace << std::endl;
+    ++localindex;
+  }
+  DoLog(2) && (Log() << Verbose(2) << "ProjectionToSubspace matrix is " << ProjectToSubspace << std::endl);
 
   // then ProjectFromSubspace is just transposed
   ProjectFromSubspace = ((const MatrixContent)ProjectToSubspace).transpose();
-  Log() << Verbose(2) << "ProjectFromSubspace matrix is " << ProjectFromSubspace << std::endl;
-}
-
-
-/** Creates the subspace matrix by projecting down the FullSpace::EigenspaceMatrix.
+  DoLog(2) && (Log() << Verbose(2) << "ProjectFromSubspace matrix is " << ProjectFromSubspace << std::endl);
+}
+
+
+/** Creates the subspace matrix by projecting down the given \a _fullmatrix.
  *  We just perform \f$M = P^t \cdot A \cdot P\f$, when P are the projection matrix,
  *  A the full matrix and M the subspace matrix.
- */
-void Subspace::projectFullSpaceMatrixToSubspace()
-{
+ *
+ *  @param _fullmatrix full matrix A to project into subspace
+ *  @return subspace matrix M
+ */
+const MatrixContent Subspace::projectFullspaceMatrixToSubspace(const MatrixContent &_fullmatrix) const
+{
+  ASSERT((FullSpace.getIndices().size() == _fullmatrix.getRows())
+      && (FullSpace.getIndices().size() == _fullmatrix.getColumns()),
+      "Subspace::projectSubspaceMatrixToFullspace() - dimensions of this subspace "
+      +toString(Indices.size())+" and the given matrix ("
+      +toString(_fullmatrix.getRows())+" x "+toString(_fullmatrix.getColumns())+") differ!");
   // construct small matrix
-  EigenspaceMatrix = ProjectFromSubspace * FullSpace.getEigenspaceMatrix() * ProjectToSubspace;
-  Log() << Verbose(2) << "EigenspaceMatrix matrix is " << EigenspaceMatrix << std::endl;
-}
-
-
-/** We associate local Eigenvectors with ones from FullSpace by a paralellity
+  MatrixContent tempMatrix = ProjectFromSubspace * _fullmatrix * ProjectToSubspace;
+  return tempMatrix;
+  DoLog(2) && (Log() << Verbose(2) << "returned subspace matrix is " << tempMatrix << std::endl);
+}
+
+
+/** Creates a full space matrix which is the projection of given \a _subspacematrix
+ * from the subspace.
+ *
+ * @param _subspacematrix subspace matrix
+ * @return full matrix of the Subspace::EigenspaceMatrix projected into
+ *         Subspace::FullSpace.
+ */
+const MatrixContent Subspace::projectSubspaceMatrixToFullspace(const MatrixContent &_subspacematrix) const
+{
+  ASSERT((Indices.size() == _subspacematrix.getRows()) && (Indices.size() == _subspacematrix.getColumns()),
+      "Subspace::projectSubspaceMatrixToFullspace() - dimensions of this subspace "
+      +toString(Indices.size())+" and the given matrix ("
+      +toString(_subspacematrix.getRows())+" x "+toString(_subspacematrix.getColumns())+") differ!");
+  return (ProjectToSubspace * _subspacematrix * ProjectFromSubspace);
+}
+
+
+/** We associate local Eigenvectors with ones from FullSpace by a parallelity
  * criterion.
  */
@@ -335 +481 @@
   for (size_t localindex = 0; localindex< Indices.size(); ++localindex) {
     boost::shared_ptr<VectorContent> &CurrentEigenvector = Eigenvectors[localindex];
-    Log() << Verbose(1) << "Current Eigenvector is " << *CurrentEigenvector << std::endl;
+    VectorContent tempCurrentEigenvector = ProjectToSubspace * (*CurrentEigenvector);
+    Log() << Verbose(1) << "Current Eigenvector is " << *CurrentEigenvector
+        << " --(projected)-> " << tempCurrentEigenvector << std::endl;
+    if (Eigenvalues[localindex] == 0) {
+      DoLog(2) && (Log() << Verbose(2) << "Is null, skipping." << std::endl);
+      continue;
+    }
 
     // (for now settle with the one we are most parallel to)
@@ -341 +493 @@
     double mostparallel_scalarproduct = 0.;
     BOOST_FOREACH( size_t indexiter, CorrespondenceList) {
-      Log() << Verbose(2) << "Comparing to old " << indexiter << "th eigenvector " << FullSpace.getEigenvector(indexiter) << std::endl;
-      const double scalarproduct = (FullSpace.getEigenvector(indexiter)) * ( ProjectToSubspace * (*CurrentEigenvector));
-      Log() << Verbose(2) << "SKP is " << scalarproduct << std::endl;
+      DoLog(2) && (Log() << Verbose(2) << "Comparing to old " << indexiter << "th eigenvector " << FullSpace.getEigenvector(indexiter) << std::endl);
+      const double scalarproduct = (FullSpace.getEigenvector(indexiter)) * ( tempCurrentEigenvector );
+      DoLog(2) && (Log() << Verbose(2) << "SKP is " << scalarproduct << std::endl);
       if (fabs(scalarproduct) > fabs(mostparallel_scalarproduct)) {
         mostparallel_scalarproduct = scalarproduct;
@@ -355 +507 @@
       if (mostparallel_scalarproduct < 0) {
         *CurrentEigenvector *= -1.;
-        Log() << Verbose(1) << "Associating (inverted) " << *CurrentEigenvector << " with " << mostparallel_index << "th's fullspace eigenvector." << std::endl;
+        DoLog(1) && (Log() << Verbose(1) << "Associating (inverted) " << *CurrentEigenvector << " with " << mostparallel_index << "th's fullspace eigenvector." << std::endl);
       } else {
-        Log() << Verbose(1) << "Associating " << *CurrentEigenvector << " with " << mostparallel_index << "th's fullspace eigenvector." << std::endl;
+        DoLog(1) && (Log() << Verbose(1) << "Associating " << *CurrentEigenvector << " with " << mostparallel_index << "th's fullspace eigenvector." << std::endl);
       }
       ASSERT( LocalToGlobal.count(localindex) == 0,