Changeset c94eeb for src/vector.cpp

Timestamp:

Jun 25, 2010, 3:27:35 PM (16 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, Candidate_v1.7.0, 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:

33d774

Parents:

325390

Message:

Replaced several double* that were used as Matrixes with actuall matrix objects

File:

• src/vector.cpp (modified) (6 diffs)

src/vector.cpp

@@ -105 +105 @@
 double Vector::PeriodicDistance(const Vector &y, const double * const cell_size) const
 {
-  double res = distance(y), tmp, matrix[NDIM*NDIM];
+  double res = distance(y), tmp;
+  Matrix matrix;
     Vector Shiftedy, TranslationVector;
     int N[NDIM];
-    matrix[0] = cell_size[0];
-    matrix[1] = cell_size[1];
-    matrix[2] = cell_size[3];
-    matrix[3] = cell_size[1];
-    matrix[4] = cell_size[2];
-    matrix[5] = cell_size[4];
-    matrix[6] = cell_size[3];
-    matrix[7] = cell_size[4];
-    matrix[8] = cell_size[5];
+    matrix.at(0,0) = cell_size[0];
+    matrix.at(1,0) = cell_size[1];
+    matrix.at(2,0) = cell_size[3];
+    matrix.at(0,1) = cell_size[1];
+    matrix.at(1,1) = cell_size[2];
+    matrix.at(2,1) = cell_size[4];
+    matrix.at(0,2) = cell_size[3];
+    matrix.at(1,2) = cell_size[4];
+    matrix.at(2,2) = cell_size[5];
     // in order to check the periodic distance, translate one of the vectors into each of the 27 neighbouring cells
     for (N[0]=-1;N[0]<=1;N[0]++)
@@ -142 +143 @@
 double Vector::PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const
 {
-  double res = DistanceSquared(y), tmp, matrix[NDIM*NDIM];
+  double res = DistanceSquared(y), tmp;
+  Matrix matrix;
     Vector Shiftedy, TranslationVector;
     int N[NDIM];
-    matrix[0] = cell_size[0];
-    matrix[1] = cell_size[1];
-    matrix[2] = cell_size[3];
-    matrix[3] = cell_size[1];
-    matrix[4] = cell_size[2];
-    matrix[5] = cell_size[4];
-    matrix[6] = cell_size[3];
-    matrix[7] = cell_size[4];
-    matrix[8] = cell_size[5];
+    matrix.at(0,0) = cell_size[0];
+    matrix.at(1,0) = cell_size[1];
+    matrix.at(2,0) = cell_size[3];
+    matrix.at(0,1) = cell_size[1];
+    matrix.at(1,1) = cell_size[2];
+    matrix.at(2,1) = cell_size[4];
+    matrix.at(0,2) = cell_size[3];
+    matrix.at(1,2) = cell_size[4];
+    matrix.at(2,2) = cell_size[5];
     // in order to check the periodic distance, translate one of the vectors into each of the 27 neighbouring cells
     for (N[0]=-1;N[0]<=1;N[0]++)
@@ -176 +178 @@
  * Tries to translate a vector into each adjacent neighbouring cell.
  */
-void Vector::KeepPeriodic(const double * const matrix)
-{
+void Vector::KeepPeriodic(const double * const _matrix)
+{
+  Matrix matrix = Matrix(_matrix);
   //  int N[NDIM];
   //  bool flag = false;
@@ -185 +188 @@
   //  Output(out);
   //  Log() << Verbose(0) << endl;
-    InverseMatrixMultiplication(matrix);
+    MatrixMultiplication(matrix.invert());
     for(int i=NDIM;i--;) { // correct periodically
       if (at(i) < 0) {  // get every coefficient into the interval [0,1)
@@ -530 +533 @@
  * \param *Minv inverse matrix
  */
-void Vector::WrapPeriodically(const double * const M, const double * const Minv)
-{
+void Vector::WrapPeriodically(const double * const _M, const double * const _Minv)
+{
+  Matrix M = Matrix(_M);
+  Matrix Minv = Matrix(_Minv);
   MatrixMultiplication(Minv);
   // truncate to [0,1] for each axis
@@ -564 +569 @@
  * \param *matrix NDIM_NDIM array
  */
-void Vector::MatrixMultiplication(const double * const M)
-{
-  (*this) *= Matrix(M);
+void Vector::MatrixMultiplication(const Matrix &M)
+{
+  (*this) *= M;
 };