Changeset d10eb6 for src

Timestamp:

Jun 26, 2010, 11:52:50 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

63d2b8

Parents:

f66b67

Message:

Made the ReturnFullMatrixForSymmetric return a Matrix object directely instead of a double array

Location:

src

Files:

• Actions/WorldAction/RepeatBoxAction.cpp (modified) (1 diff)
• Matrix.cpp (modified) (1 diff)
• Matrix.hpp (modified) (1 diff)
• analysis_correlation.cpp (modified) (3 diffs)
• boundary.cpp (modified) (1 diff)
• helpers.cpp (modified) (1 diff)
• helpers.hpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (1 diff)
• molecule_geometry.cpp (modified) (5 diffs)

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -61 +61 @@
     (cout << "Repeating box " << Repeater << " times for (x,y,z) axis." << endl);
     double * const cell_size = World::getInstance().getDomain();
-    double *M_double = ReturnFullMatrixforSymmetric(cell_size);
-    Matrix M = Matrix(M_double);
-    delete[] M_double;
+    Matrix M = ReturnFullMatrixforSymmetric(cell_size);
     Vector x,y;
     int n[NDIM];

src/Matrix.cpp

@@ -135 +135 @@
   return factor*mat;
 }
+
+/** Blows the 6-dimensional \a cell_size array up to a full NDIM by NDIM matrix.
+ * \param *symm 6-dim array of unique symmetric matrix components
+ * \return allocated NDIM*NDIM array with the symmetric matrix
+ */
+Matrix ReturnFullMatrixforSymmetric(const double * const symm)
+{
+  Matrix matrix;
+  matrix.at(0,0) = symm[0];
+  matrix.at(1,0) = symm[1];
+  matrix.at(2,0) = symm[3];
+  matrix.at(0,1) = symm[1];
+  matrix.at(1,1) = symm[2];
+  matrix.at(2,1) = symm[4];
+  matrix.at(0,2) = symm[3];
+  matrix.at(1,2) = symm[4];
+  matrix.at(2,2) = symm[5];
+  return matrix;
+};

src/Matrix.hpp

@@ -50 +50 @@
 Matrix operator*(const Matrix&,const double);
 
+Matrix ReturnFullMatrixforSymmetric(const double * const cell_size);
+
 #endif /* MATRIX_HPP_ */

src/analysis_correlation.cpp

@@ -136 +136 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++){
     if ((*MolWalker)->ActiveFlag) {
-      double * FullMatrix_double = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-      Matrix FullMatrix = Matrix(FullMatrix_double);
+      Matrix FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
       Matrix FullInverseMatrix = FullMatrix.invert();
-      delete[](FullMatrix_double);
       DoeLog(2) && (eLog()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
       eLog() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
@@ -247 +245 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      double * FullMatrix_double = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-      Matrix FullMatrix = Matrix(FullMatrix_double);
+      Matrix FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
       Matrix FullInverseMatrix = FullMatrix.invert();
-      delete[] FullMatrix_double;
       DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
       for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
@@ -353 +349 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      double * FullMatrix_double = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-      Matrix FullMatrix = Matrix(FullMatrix_double);
+      Matrix FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
       Matrix FullInverseMatrix = FullMatrix.invert();
-      delete[](FullMatrix_double);
       DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
       for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {

src/boundary.cpp

@@ -765 +765 @@
   int N[NDIM];
   int n[NDIM];
-  double *M_double =  ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-  Matrix M = Matrix(M_double);
-  delete[](M_double);
+  Matrix M = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
   Matrix Rotations;
   Matrix MInverse = M.invert();

src/helpers.cpp

@@ -117 +117 @@
 };
 
-/** Blows the 6-dimensional \a cell_size array up to a full NDIM by NDIM matrix.
- * \param *symm 6-dim array of unique symmetric matrix components
- * \return allocated NDIM*NDIM array with the symmetric matrix
- */
-double * ReturnFullMatrixforSymmetric(const double * const symm)
-{
-  double *matrix = new double[NDIM * NDIM];
-  matrix[0] = symm[0];
-  matrix[1] = symm[1];
-  matrix[2] = symm[3];
-  matrix[3] = symm[1];
-  matrix[4] = symm[2];
-  matrix[5] = symm[4];
-  matrix[6] = symm[3];
-  matrix[7] = symm[4];
-  matrix[8] = symm[5];
-  return matrix;
-};
-
-
 /** Comparison function for GSL heapsort on distances in two molecules.
  * \param *a

src/helpers.hpp

@@ -52 +52 @@
 bool IsValidNumber( const char *string);
 int CompareDoubles (const void * a, const void * b);
-double * ReturnFullMatrixforSymmetric(const double * const cell_size);
 void performCriticalExit();
 

src/molecule.cpp

@@ -308 +308 @@
       } // (signs are correct, was tested!)
     }
-    double *matrix_double = ReturnFullMatrixforSymmetric(cell_size);
-    matrix = Matrix(matrix_double);
-    delete[](matrix_double);
+    matrix = ReturnFullMatrixforSymmetric(cell_size);
     Orthovector1.MatrixMultiplication(matrix);
     InBondvector -= Orthovector1; // subtract just the additional translation

src/molecule_fragmentation.cpp

@@ -1710 +1710 @@
   atom *OtherWalker = NULL;
   double * const cell_size = World::getInstance().getDomain();
-  double *matrix_double = ReturnFullMatrixforSymmetric(cell_size);
-  Matrix matrix = Matrix(matrix_double);
-  delete[](matrix_double);
+  Matrix matrix = ReturnFullMatrixforSymmetric(cell_size);
   enum Shading *ColorList = NULL;
   double tmp;

src/molecule_geometry.cpp

@@ -35 +35 @@
   const Vector *CenterBox = DetermineCenterOfBox();
   double * const cell_size = World::getInstance().getDomain();
-  double *M_double = ReturnFullMatrixforSymmetric(cell_size);
-  Matrix M = Matrix(M_double);
-  delete[](M_double);
+  Matrix M = ReturnFullMatrixforSymmetric(cell_size);
   Matrix Minv = M.invert();
 
@@ -59 +57 @@
   bool status = true;
   double * const cell_size = World::getInstance().getDomain();
-  double *M_double = ReturnFullMatrixforSymmetric(cell_size);
-  Matrix M = Matrix(M_double);
-  delete[](M_double);
+  Matrix M = ReturnFullMatrixforSymmetric(cell_size);
   Matrix Minv = M.invert();
 
@@ -159 +155 @@
 
   const double *cell_size = World::getInstance().getDomain();
-  double *M_double = ReturnFullMatrixforSymmetric(cell_size);
-  Matrix M = Matrix(M_double);
-  delete[](M_double);
+  Matrix M = ReturnFullMatrixforSymmetric(cell_size);
   a->MatrixMultiplication(M);
 
@@ -250 +244 @@
 {
   double * const cell_size = World::getInstance().getDomain();
-  double *M_double = ReturnFullMatrixforSymmetric(cell_size);
-  Matrix M = Matrix(M_double);
-  delete[](M_double);
+  Matrix M = ReturnFullMatrixforSymmetric(cell_size);
   Matrix Minv = M.invert();
 
@@ -282 +274 @@
 {
   double * const cell_size = World::getInstance().getDomain();
-  double *matrix_double = ReturnFullMatrixforSymmetric(cell_size);
-  Matrix matrix = Matrix(matrix_double);
-  delete[](matrix_double);
+  Matrix matrix = ReturnFullMatrixforSymmetric(cell_size);
   Matrix inversematrix = matrix.invert();
   double tmp;