Changeset d0f111 for src

Timestamp:

Jun 26, 2010, 11:33:17 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:

f66b67

Parents:

2f1a7a

Message:

Changed Vector::WrapPeriodically to use matrixes instead of double*

Location:

src

Files:

• molecule_geometry.cpp (modified) (4 diffs)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/molecule_geometry.cpp

@@ -35 +35 @@
   const Vector *CenterBox = DetermineCenterOfBox();
   double * const cell_size = World::getInstance().getDomain();
-  double *M = ReturnFullMatrixforSymmetric(cell_size);
-  double *Minv = InverseMatrix(M);
+  double *M_double = ReturnFullMatrixforSymmetric(cell_size);
+  Matrix M = Matrix(M_double);
+  delete[](M_double);
+  Matrix Minv = M.invert();
 
   // go through all atoms
   ActOnAllVectors( &Vector::SubtractVector, *Center);
   ActOnAllVectors( &Vector::SubtractVector, *CenterBox);
-  ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
-
-  delete[](M);
-  delete[](Minv);
+  BOOST_FOREACH(atom* iter, atoms){
+    iter->node->WrapPeriodically(M, Minv);
+  }
+
   delete(Center);
   return status;
@@ -57 +59 @@
   bool status = true;
   double * const cell_size = World::getInstance().getDomain();
-  double *M = ReturnFullMatrixforSymmetric(cell_size);
-  double *Minv = InverseMatrix(M);
+  double *M_double = ReturnFullMatrixforSymmetric(cell_size);
+  Matrix M = Matrix(M_double);
+  delete[](M_double);
+  Matrix Minv = M.invert();
 
   // go through all atoms
-  ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
-
-  delete[](M);
-  delete[](Minv);
+  BOOST_FOREACH(atom* iter, atoms){
+    iter->node->WrapPeriodically(M, Minv);
+  }
+
   return status;
 };
@@ -246 +250 @@
 {
   double * const cell_size = World::getInstance().getDomain();
-  double *M = ReturnFullMatrixforSymmetric(cell_size);
-  double *Minv = InverseMatrix(M);
+  double *M_double = ReturnFullMatrixforSymmetric(cell_size);
+  Matrix M = Matrix(M_double);
+  delete[](M_double);
+  Matrix Minv = M.invert();
 
   // go through all atoms
   ActOnAllVectors( &Vector::AddVector, *trans);
-  ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
-
-  delete[](M);
-  delete[](Minv);
+  BOOST_FOREACH(atom* iter, atoms){
+    iter->node->WrapPeriodically(M, Minv);
+  }
+
 };
 
@@ -265 +271 @@
   OBSERVE;
   Plane p(*n,0);
-  BOOST_FOREACH( atom* iter, atoms ){
+  BOOST_FOREACH(atom* iter, atoms ){
     (*iter->node) = p.mirrorVector(*iter->node);
   }

src/vector.cpp

@@ -533 +533 @@
  * \param *Minv inverse matrix
  */
-void Vector::WrapPeriodically(const double * const _M, const double * const _Minv)
-{
-  Matrix M = Matrix(_M);
-  Matrix Minv = Matrix(_Minv);
+void Vector::WrapPeriodically(const Matrix &M, const Matrix &Minv)
+{
   MatrixMultiplication(Minv);
   // truncate to [0,1] for each axis

src/vector.hpp

@@ -65 +65 @@
   bool MakeNormalTo(const Vector &y1);
   bool IsInParallelepiped(const Vector &offset, const double * const parallelepiped) const;
-  void WrapPeriodically(const double * const M, const double * const Minv);
+  void WrapPeriodically(const Matrix &M, const Matrix &Minv);
   std::pair<Vector,Vector> partition(const Vector&) const;
   std::pair<pointset,Vector> partition(const pointset&) const;