Changeset f5bca2

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:

9c5296

Parents:

742371

git-author:

Frederik Heber <heber@…> (11/22/10 11:10:57)

git-committer:

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

Message:

SubspaceFactorizer now has the matrix dimension as an enum.

Location:

src/unittests

Files:

• SubspaceFactorizerUnittest.cpp (modified) (11 diffs)
• SubspaceFactorizerUnittest.hpp (modified) (1 diff)

src/unittests/SubspaceFactorizerUnittest.cpp

@@ -45 +45 @@
 
 void SubspaceFactorizerUnittest::setUp(){
-  fourbyfour = new MatrixContent(4,4);
-  fourbyfour->setZero();
-  for (int i=0; i<4 ; i++) {
-    fourbyfour->set(i,i, 2.);
-    if (i < (4-1)) {
-      fourbyfour->set(i+1,i, 1.);
-      fourbyfour->set(i,i+1, 1.);
-    }
-  }
-  transformation = new MatrixContent**[3];
-
-  // 1d subspace
-  transformation[0] = new MatrixContent*[4];
-  for(size_t i=0; i<4;++i) {
-    transformation[0][i] = new MatrixContent(4,4);
-    transformation[0][i]->setZero();
-    for (size_t j=0; j<1; ++j)
-      transformation[0][i]->set(i+j,i+j, 1.);
-//    std::cout << i << "th transformation matrix, " << 1 << "d subspace is "
-//        << *transformation[0][i] << std::endl;
-  }
-
-  // 2d subspace
-  transformation[1] = new MatrixContent*[3];
-  for(size_t i=0; i<3;++i) {
-    transformation[1][i] = new MatrixContent(4,4);
-    transformation[1][i]->setZero();
-    for (size_t j=0; j<2; ++j)
-      transformation[1][i]->set(i+j,i+j, 1.);
-//    std::cout << i << "th transformation matrix, " << 2 << "d subspace is "
-//        << *transformation[1][i] << std::endl;
-  }
-
-  // 3d subspace
-  transformation[2] = new MatrixContent*[2];
-  for(size_t i=0; i<2;++i) {
-    transformation[2][i] = new MatrixContent(4,4);
-    transformation[2][i]->setZero();
-    for (size_t j=0; j<3; ++j)
-      transformation[2][i]->set(i+j,i+j, 1.);
-//    std::cout << i << "th transformation matrix, " << 3 << "d subspace is "
-//        << *transformation[2][i] << std::endl;
-  }
-}
+  matrix = new MatrixContent(matrixdimension,matrixdimension);
+  matrix->setZero();
+  for (int i=0; i<matrixdimension ; i++) {
+    matrix->set(i,i, 2.);
+    if (i < (matrixdimension-1)) {
+      matrix->set(i+1,i, 1.);
+      matrix->set(i,i+1, 1.);
+    }
+  }
+}
+
 void SubspaceFactorizerUnittest::tearDown(){
   // delete test matrix
-  delete fourbyfour;
-
-  // delete all transformations
-  for(size_t i=0; i<3;++i)
-    delete transformation[0][i];
-  delete[] transformation[0];
-  for(size_t i=0; i<3;++i)
-    delete transformation[1][i];
-  delete[] transformation[1];
-  for(size_t i=0; i<2;++i)
-    delete transformation[2][i];
-  delete[] transformation[2];
-  delete[] transformation;
+  delete matrix;
 }
 
 void SubspaceFactorizerUnittest::BlockTest()
 {
-  MatrixContent temp((*fourbyfour)&(*transformation[0][0]));
-  std::cout << "Our matrix is " << *fourbyfour << "." << std::endl;
-
-  std::cout << "Hadamard product of " << *fourbyfour << " with " << *transformation[0][0] << " is: " << std::endl;
+  MatrixContent *transformation = new MatrixContent(matrixdimension,matrixdimension);
+  transformation->setZero();
+  for (size_t j=0; j<1; ++j)
+    transformation->set(j,j, 1.);
+
+  MatrixContent temp((*matrix)&(*transformation));
+  std::cout << "Our matrix is " << *matrix << "." << std::endl;
+
+  std::cout << "Hadamard product of " << *matrix << " with " << *transformation << " is: " << std::endl;
   std::cout << temp << std::endl;
 
@@ -120 +80 @@
   delete eigenvaluesView;
   gsl_vector_free(eigenvalues);
+  delete (transformation);
 
 
@@ -329 +290 @@
 
   // (for now settle with the one we are most parallel to)
-  size_t mostparallel_index = 4;
+  size_t mostparallel_index = SubspaceFactorizerUnittest::matrixdimension;
   double mostparallel_scalarproduct = 0.;
   BOOST_FOREACH( size_t indexiter, CorrespondenceList) {
@@ -340 +301 @@
     }
   }
-  if (mostparallel_index != 4) {
+  if (mostparallel_index != SubspaceFactorizerUnittest::matrixdimension) {
     // put into std::list for later use
     // invert if pointing in negative direction
@@ -358 +319 @@
   VectorArray CurrentEigenvectors;
   ValueArray CurrentEigenvalues;
-  VectorValueList *ParallelEigenvectorList = new VectorValueList[4];
+  VectorValueList *ParallelEigenvectorList = new VectorValueList[matrixdimension];
   IndexSet AllIndices;
 
   // create the total index set
-  for (size_t i=0;i<4;++i)
+  for (size_t i=0;i<matrixdimension;++i)
     AllIndices.insert(i);
 
@@ -368 +329 @@
   IndexMap Dimension_to_Indexset;
   for (size_t dim = 0; dim<3;++dim) {
-    for (size_t i=0;i<4-dim;++i) {
+    for (size_t i=0;i<matrixdimension;++i) {
       IndexSet *indexset = new IndexSet;
-      for (size_t j=0;j<=dim;++j) {
-        //std::cout << "Putting " << i+j << " into " << i << "th map " << dim << std::endl;
-        CPPUNIT_ASSERT_MESSAGE("index "+toString(i+j)+" already present in "+toString(dim)+"-dim "+toString(i)+"th indexset.", indexset->count(i+j) == 0);
-        indexset->insert(i+j);
+      for (size_t j=0;j<dim+1;++j) {
+        const int value = (i+j) % matrixdimension;
+        //std::cout << "Putting " << value << " into " << i << "th map " << dim << std::endl;
+        CPPUNIT_ASSERT_MESSAGE("index "+toString(value)+" already present in "+toString(dim)+"-dim "+toString(i)+"th indexset.", indexset->count(value) == 0);
+        indexset->insert(value);
       }
       Dimension_to_Indexset.insert( make_pair(dim, boost::shared_ptr<IndexSet>(indexset)) );
@@ -381 +343 @@
   }
 
-  // set to first guess, i.e. the unit vectors of R^4
+  // set to first guess, i.e. the unit vectors of R^matrixdimension
   BOOST_FOREACH( size_t index, AllIndices) {
-    boost::shared_ptr<VectorContent> EV(new VectorContent(4));
+    boost::shared_ptr<VectorContent> EV(new VectorContent(matrixdimension));
     EV->setZero();
     EV->at(index) = 1.;
@@ -392 +354 @@
   size_t run=1; // counting iterations
   double threshold = 1.;  // containing threshold value
-  while ((threshold > 1e-6) && (run < 200)) {
+  while ((threshold > 1e-10) && (run < 200)) {
     // for every dimension
-    for (size_t dim = 0; dim<3;++dim) {
+    for (size_t dim = 0; dim<4;++dim) {
       // for every index set of this dimension
       Log() << Verbose(0) << std::endl << std::endl;
@@ -407 +369 @@
 
         // create transformation matrices from these
-        MatrixContent *subsystem = getSubspaceMatrix(*fourbyfour, CurrentEigenvectors, *(IndexsetIter->second));
+        MatrixContent *subsystem = getSubspaceMatrix(*matrix, CurrentEigenvectors, *(IndexsetIter->second));
         Log() << Verbose(2) << "Subsystem matrix is " << *subsystem << std::endl;
 
@@ -415 +377 @@
         Log() << Verbose(2) << "Eigenvalues are " << *Eigenvalues << std::endl;
 
-        // blow up eigenvectors to 4dim column vector again
+        // blow up eigenvectors to matrixdimensiondim column vector again
         MatrixContent *Eigenvectors = embedSubspaceMatrix(CurrentEigenvectors, *subsystem, *(IndexsetIter->second));
-        Log() << Verbose(1) << "4x4 Eigenvector matrix is " << *Eigenvectors << std::endl;
+        Log() << Verbose(1) << matrixdimension << "x" << matrixdimension << " Eigenvector matrix is " << *Eigenvectors << std::endl;
 
         // we don't need the subsystem anymore
@@ -488 +450 @@
     }
 
-    // check orthonormality again
-    checkOrthogonality(AllIndices, CurrentEigenvectors);
+//    // check orthonormality again
+//    checkOrthogonality(AllIndices, CurrentEigenvectors);
 
     // show new ones

src/unittests/SubspaceFactorizerUnittest.hpp

@@ -34 +34 @@
   void EigenvectorTest();
 
-  MatrixContent *fourbyfour;
+  enum { matrixdimension = 3 };
+private:
+
+  MatrixContent *matrix;
 
   MatrixContent ***transformation;