Changeset 5108e1

Timestamp:

Jun 30, 2010, 9:00:19 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:

1da5f5

Parents:

4d206f

Message:

Removed MatrixMultiplication() method from Vector class

Location:

src

Files:

• Actions/WorldAction/RepeatBoxAction.cpp (modified) (1 diff)
• analysis_correlation.cpp (modified) (5 diffs)
• boundary.cpp (modified) (3 diffs)
• ellipsoid.cpp (modified) (2 diffs)
• molecule.cpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (1 diff)
• molecule_geometry.cpp (modified) (5 diffs)
• vector.cpp (modified) (5 diffs)
• vector.hpp (modified) (1 diff)

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -99 +99 @@
                 DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
               x = y;
-              x.MatrixMultiplication(M);
+              x *= M;
               newmol = World::getInstance().createMolecule();
               molecules->insert(newmol);

src/analysis_correlation.cpp

@@ -142 +142 @@
       for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
         DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-        periodicX = *(*iter)->node;
-        periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
+        periodicX = FullInverseMatrix * (*(*iter)->node); // x now in [0,1)^3
         // go through every range in xyz and get distance
         for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
           for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
             for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-              checkX = Vector(n[0], n[1], n[2]) + periodicX;
-              checkX.MatrixMultiplication(FullMatrix);
+              checkX = FullMatrix * (Vector(n[0], n[1], n[2]) + periodicX);
               for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++){
                 if ((*MolOtherWalker)->ActiveFlag) {
@@ -158 +156 @@
                       for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
                         if ((PairRunner->first == (**iter).type) && (PairRunner->second == (**runner).type)) {
-                          periodicOtherX = *(*runner)->node;
-                          periodicOtherX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
+                          periodicOtherX = FullInverseMatrix * (*(*runner)->node); // x now in [0,1)^3
                           // go through every range in xyz and get distance
                           for (Othern[0]=-ranges[0]; Othern[0] <= ranges[0]; Othern[0]++)
                             for (Othern[1]=-ranges[1]; Othern[1] <= ranges[1]; Othern[1]++)
                               for (Othern[2]=-ranges[2]; Othern[2] <= ranges[2]; Othern[2]++) {
-                                checkOtherX = Vector(Othern[0], Othern[1], Othern[2]) + periodicOtherX;
-                                checkOtherX.MatrixMultiplication(FullMatrix);
+                                checkOtherX = FullMatrix * (Vector(Othern[0], Othern[1], Othern[2]) + periodicOtherX);
                                 distance = checkX.distance(checkOtherX);
                                 //Log() << Verbose(1) <<"Inserting " << *(*iter) << " and " << *(*runner) << endl;
@@ -252 +248 @@
         for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
           if ((*type == NULL) || ((*iter)->type == *type)) {
-            periodicX = *(*iter)->node;
-            periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
+            periodicX = FullInverseMatrix * (*(*iter)->node); // x now in [0,1)^3
             // go through every range in xyz and get distance
             for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
               for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
                 for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                  checkX = Vector(n[0], n[1], n[2]) + periodicX;
-                  checkX.MatrixMultiplication(FullMatrix);
+                  checkX = FullMatrix * (Vector(n[0], n[1], n[2]) + periodicX);
                   distance = checkX.distance(*point);
                   DoLog(4) && (Log() << Verbose(4) << "Current distance is " << distance << "." << endl);
@@ -356 +350 @@
         for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
           if ((*type == NULL) || ((*iter)->type == *type)) {
-            periodicX = *(*iter)->node;
-            periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
+            periodicX = FullInverseMatrix * (*(*iter)->node); // x now in [0,1)^3
             // go through every range in xyz and get distance
             ShortestDistance = -1.;
@@ -363 +356 @@
               for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
                 for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                  checkX = Vector(n[0], n[1], n[2]) + periodicX;
-                  checkX.MatrixMultiplication(FullMatrix);
+                  checkX = FullMatrix * (Vector(n[0], n[1], n[2]) + periodicX);
                   TriangleIntersectionList Intersections(&checkX,Surface,LC);
                   distance = Intersections.GetSmallestDistance();

src/boundary.cpp

@@ -800 +800 @@
 
   // calculate filler grid in [0,1]^3
-  FillerDistance = Vector(distance[0], distance[1], distance[2]);
-  FillerDistance.MatrixMultiplication(MInverse);
+  FillerDistance = MInverse * Vector(distance[0], distance[1], distance[2]);
   for(int i=0;i<NDIM;i++)
     N[i] = (int) ceil(1./FillerDistance[i]);
@@ -814 +813 @@
       for (n[2] = 0; n[2] < N[2]; n[2]++) {
         // calculate position of current grid vector in untransformed box
-        CurrentPosition = Vector((double)n[0]/(double)N[0], (double)n[1]/(double)N[1], (double)n[2]/(double)N[2]);
-        CurrentPosition.MatrixMultiplication(M);
+        CurrentPosition = M * Vector((double)n[0]/(double)N[0], (double)n[1]/(double)N[1], (double)n[2]/(double)N[2]);
         // create molecule random translation vector ...
         for (int i=0;i<NDIM;i++)
@@ -850 +848 @@
           Inserter = (*iter)->x;
           if (DoRandomRotation)
-            Inserter.MatrixMultiplication(Rotations);
+            Inserter *= Rotations;
           Inserter += AtomTranslations + FillerTranslations + CurrentPosition;
 
           // check whether inserter is inside box
-          Inserter.MatrixMultiplication(MInverse);
+          Inserter *= MInverse;
           FillIt = true;
           for (int i=0;i<NDIM;i++)
             FillIt = FillIt && (Inserter[i] >= -MYEPSILON) && ((Inserter[i]-1.) <= MYEPSILON);
-          Inserter.MatrixMultiplication(M);
+          Inserter *= M;
 
           // Check whether point is in- or outside

src/ellipsoid.cpp

@@ -61 +61 @@
   Matrix.set(1,2, sin(theta)*cos(phi));
   Matrix.set(2,2, cos(theta));
-  helper.MatrixMultiplication(Matrix);
+  helper *= Matrix;
   helper.ScaleAll(InverseLength);
   //Log() << Verbose(4) << "Transformed RefPoint is at " << helper << "." << endl;
@@ -83 +83 @@
   Matrix.set(1,2, sin(theta)*cos(phi));
   Matrix.set(2,2, cos(theta));
-  helper.MatrixMultiplication(Matrix);
+  helper *= Matrix;
   //Log() << Verbose(4) << "Intersection is at " << helper << "." << endl;
 

src/molecule.cpp

@@ -309 +309 @@
     }
     matrix = ReturnFullMatrixforSymmetric(cell_size);
-    Orthovector1.MatrixMultiplication(matrix);
+    Orthovector1 *= matrix;
     InBondvector -= Orthovector1; // subtract just the additional translation
     bondlength = InBondvector.Norm();

src/molecule_fragmentation.cpp

@@ -1750 +1750 @@
           Translationvector[i] = (tmp < 0) ? +1. : -1.;
       }
-      Translationvector.MatrixMultiplication(matrix);
+      Translationvector *= matrix;
       //Log() << Verbose(3) << "Translation vector is ";
       Log() << Verbose(0) << Translationvector <<  endl;

src/molecule_geometry.cpp

@@ -156 +156 @@
   const double *cell_size = World::getInstance().getDomain();
   Matrix M = ReturnFullMatrixforSymmetric(cell_size);
-  a->MatrixMultiplication(M);
+  (*a) *= M;
 
   return a;
@@ -287 +287 @@
       if ((*iter)->type->Z != 1) {
 #endif
-        Testvector = (*iter)->x;
-        Testvector.MatrixMultiplication(inversematrix);
+        Testvector = inversematrix * (*iter)->x;
         Translationvector.Zero();
         for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
@@ -305 +304 @@
         }
         Testvector += Translationvector;
-        Testvector.MatrixMultiplication(matrix);
+        Testvector *= matrix;
         Center += Testvector;
         Log() << Verbose(1) << "vector is: " << Testvector << endl;
@@ -312 +311 @@
         for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
           if ((*Runner)->GetOtherAtom((*iter))->type->Z == 1) {
-            Testvector = (*Runner)->GetOtherAtom((*iter))->x;
-            Testvector.MatrixMultiplication(inversematrix);
+            Testvector = inversematrix * (*Runner)->GetOtherAtom((*iter))->x;
             Testvector += Translationvector;
-            Testvector.MatrixMultiplication(matrix);
+            Testvector *= matrix;
             Center += Testvector;
             Log() << Verbose(1) << "Hydrogen vector is: " << Testvector << endl;
@@ -386 +384 @@
     // the eigenvectors specify the transformation matrix
     Matrix M = Matrix(evec->data);
-    ActOnAllVectors( &Vector::MatrixMultiplication, static_cast<const Matrix>(M));
+    BOOST_FOREACH(atom* iter, atoms){
+      (*iter->node) *= M;
+    }
     DoLog(0) && (Log() << Verbose(0) << "done." << endl);
 

src/vector.cpp

@@ -125 +125 @@
         for (N[2]=-1;N[2]<=1;N[2]++) {
           // create the translation vector
-          TranslationVector.Zero();
-          for (int i=NDIM;i--;)
-            TranslationVector[i] = (double)N[i];
-          TranslationVector.MatrixMultiplication(matrix);
+          TranslationVector = matrix * Vector(N[0],N[1],N[2]);
           // add onto the original vector to compare with
           Shiftedy = y + TranslationVector;
@@ -470 +467 @@
 void Vector::WrapPeriodically(const Matrix &M, const Matrix &Minv)
 {
-  MatrixMultiplication(Minv);
+  *this *= Minv;
   // truncate to [0,1] for each axis
   for (int i=0;i<NDIM;i++) {
@@ -479 +476 @@
       at(i) += 1.;
   }
-  MatrixMultiplication(M);
+  *this *= M;
 };
 
@@ -498 +495 @@
   return make_pair(res,helper);
 }
-
-/** Do a matrix multiplication.
- * \param *matrix NDIM_NDIM array
- */
-void Vector::MatrixMultiplication(const Matrix &M)
-{
-  (*this) *= M;
-};
 
 /** Creates this vector as the b y *factors' components scaled linear combination of the given three.
@@ -615 +604 @@
 bool Vector::IsInParallelepiped(const Vector &offset, const double * const _parallelepiped) const
 {
-  Vector a = (*this)-offset;
   Matrix parallelepiped = Matrix(_parallelepiped).invert();
-  a.MatrixMultiplication(parallelepiped);
+  Vector a = parallelepiped * ((*this)-offset);
   bool isInside = true;
 

src/vector.hpp

@@ -60 +60 @@
   void ScaleAll(const double *factor);
   void Scale(const double factor);
-  void MatrixMultiplication(const Matrix &M);
   bool GetOneNormalVector(const Vector &x1);
   bool MakeNormalTo(const Vector &y1);