Changeset 4b0cbb for src

Timestamp:

Jun 30, 2010, 10:47:06 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:

9df5c6

Parents:

7579a4b

Message:

Made the Vector::PeriodicDistance() and Vector::PeriodicDistanceSquared() methods take Matrices instead of double *

Location:

src

Files:

• molecule_graph.cpp (modified) (3 diffs)
• vector.cpp (modified) (3 diffs)
• vector.hpp (modified) (1 diff)

src/molecule_graph.cpp

@@ -24 +24 @@
 #include "Helpers/fast_functions.hpp"
 #include "Helpers/Assert.hpp"
+#include "Matrix.hpp"
 
 
@@ -122 +123 @@
   bool free_BG = false;
   double * const cell_size = World::getInstance().getDomain();
+  Matrix M = ReturnFullMatrixforSymmetric(cell_size);
 
   if (BG == NULL) {
@@ -178 +180 @@
                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                           (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
-                          const double distance = OtherWalker->x.PeriodicDistanceSquared(Walker->x,cell_size);
+                          const double distance = OtherWalker->x.PeriodicDistanceSquared(Walker->x,M);
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
 //                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;

src/vector.cpp

@@ -103 +103 @@
  * \return \f$| x - y |\f$
  */
-double Vector::PeriodicDistance(const Vector &y, const double * const cell_size) const
+double Vector::PeriodicDistance(const Vector &y, const Matrix &cell_size) const
 {
   return sqrt(PeriodicDistanceSquared(y,cell_size));
@@ -113 +113 @@
  * \return \f$| x - y |^2\f$
  */
-double Vector::PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const
+double Vector::PeriodicDistanceSquared(const Vector &y, const Matrix &cell_size) const
 {
   double res = DistanceSquared(y), tmp;
-  Matrix matrix = ReturnFullMatrixforSymmetric(cell_size);
     Vector Shiftedy, TranslationVector;
     int N[NDIM];
@@ -125 +124 @@
         for (N[2]=-1;N[2]<=1;N[2]++) {
           // create the translation vector
-          TranslationVector = matrix * Vector(N[0],N[1],N[2]);
+          TranslationVector = cell_size * Vector(N[0],N[1],N[2]);
           // add onto the original vector to compare with
           Shiftedy = y + TranslationVector;

src/vector.hpp

@@ -43 +43 @@
   double DistanceSquared(const Vector &y) const;
   double DistanceToSpace(const Space& space) const;
-  double PeriodicDistance(const Vector &y, const double * const cell_size) const;
-  double PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const;
+  double PeriodicDistance(const Vector &y, const Matrix &cell_size) const;
+  double PeriodicDistanceSquared(const Vector &y, const Matrix &cell_size) const;
   double ScalarProduct(const Vector &y) const;
   double Angle(const Vector &y) const;