Changeset 014475

Timestamp:

Jul 1, 2010, 1:44:39 PM (14 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:

8f822c

Parents:

12cf773

Message:

Made all places use the periodicDistance() and periodicDistanceSquared() methods provided by the Box class

Location:

src

Files:

• Box.cpp (modified) (3 diffs)
• Box.hpp (modified) (1 diff)
• VectorSet.hpp (modified) (1 diff)
• analysis_correlation.cpp (modified) (4 diffs)
• molecule_graph.cpp (modified) (2 diffs)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/Box.cpp

@@ -51 +51 @@
 }
 
-Vector Box::translateIn(const Vector &point){
+Vector Box::translateIn(const Vector &point) const{
   return (*M) * point;
 }
 
-Vector Box::translateOut(const Vector &point){
+Vector Box::translateOut(const Vector &point) const{
   return (*Minv) * point;
 }
 
-Vector Box::WrapPeriodically(const Vector &point){
+Vector Box::WrapPeriodically(const Vector &point) const{
   Vector helper = translateOut(point);
   for(int i=NDIM;i--;){
@@ -71 +71 @@
 }
 
-VECTORSET(std::list) Box::explode(const Vector &point){
+VECTORSET(std::list) Box::explode(const Vector &point) const{
   VECTORSET(std::list) res;
 
@@ -91 +91 @@
 }
 
-double Box::periodicDistanceSquared(const Vector &point1,const Vector &point2){
-  VectorSet<std::list<Vector> > expansion = explode(point1);
-  return expansion.minDistSquared(point2);
+double Box::periodicDistanceSquared(const Vector &point1,const Vector &point2) const{
+  VECTORSET(std::list) expansion = explode(point1);
+  double res = expansion.minDistSquared(point2);
+  return res;
+}
+
+double Box::periodicDistance(const Vector &point1,const Vector &point2) const{
+  double res;
+  res = sqrt(periodicDistanceSquared(point1,point2));
+  return res;
 }
 

src/Box.hpp

@@ -29 +29 @@
   Box &operator=(const Matrix&);
 
-  Vector translateIn(const Vector &point);
-  Vector translateOut(const Vector &point);
+  Vector translateIn(const Vector &point) const;
+  Vector translateOut(const Vector &point) const;
 
-  Vector WrapPeriodically(const Vector &point);
-  VECTORSET(std::list) explode(const Vector &point);
+  Vector WrapPeriodically(const Vector &point) const;
+  VECTORSET(std::list) explode(const Vector &point) const;
 
-  double periodicDistanceSquared(const Vector &point1,const Vector &point2);
+  double periodicDistanceSquared(const Vector &point1,const Vector &point2) const;
+  double periodicDistance(const Vector &point1,const Vector &point2) const;
 
 private:

src/VectorSet.hpp

@@ -57 +57 @@
       return std::numeric_limits<double>::infinity();
     std::list<double> helper;
+    helper.resize(this->size());
     transform(this->begin(),this->end(),
               helper.begin(),

src/analysis_correlation.cpp

@@ -36 +36 @@
   PairCorrelationMap *outmap = NULL;
   double distance = 0.;
-  const Matrix &domain = World::getInstance().getDomain().getM();
+  Box &domain = World::getInstance().getDomain();
 
   if (molecules->ListOfMolecules.empty()) {
@@ -77 +77 @@
                 for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
                   if ((PairRunner->first == (**iter).type) && (PairRunner->second == (**runner).type)) {
-                    distance = (*iter)->node->PeriodicDistance(*(*runner)->node,  domain);
+                    distance = domain.periodicDistance(*(*iter)->node,*(*runner)->node);
                     //Log() << Verbose(1) <<"Inserting " << *(*iter) << " and " << *(*runner) << endl;
                     outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
@@ -191 +191 @@
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
-  const Matrix &domain = World::getInstance().getDomain().getM();
+  Box &domain = World::getInstance().getDomain();
 
   if (molecules->ListOfMolecules.empty()) {
@@ -207 +207 @@
         for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
           if ((*type == NULL) || ((*iter)->type == *type)) {
-            distance = (*iter)->node->PeriodicDistance(*point, domain);
+            distance = domain.periodicDistance(*(*iter)->node,*point);
             DoLog(4) && (Log() << Verbose(4) << "Current distance is " << distance << "." << endl);
             outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> ((*iter), point) ) );

src/molecule_graph.cpp

@@ -123 +123 @@
   LinkedCell *LC = NULL;
   bool free_BG = false;
-  const Matrix &M = World::getInstance().getDomain().getM();
+  Box &domain = World::getInstance().getDomain();
 
   if (BG == NULL) {
@@ -180 +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,M);
+                          const double distance = domain.periodicDistanceSquared(OtherWalker->x,Walker->x);
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
 //                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;

src/vector.cpp

@@ -97 +97 @@
   return *this;
 }
-
-/** Calculates distance between this and another vector in a periodic cell.
- * \param *y array to second vector
- * \param *cell_size 6-dimensional array with (xx, xy, yy, xz, yz, zz) entries specifying the periodic cell
- * \return \f$| x - y |\f$
- */
-double Vector::PeriodicDistance(const Vector &y, const Matrix &cell_size) const
-{
-  return sqrt(PeriodicDistanceSquared(y,cell_size));
-};
-
-/** Calculates distance between this and another vector in a periodic cell.
- * \param *y array to second vector
- * \param *cell_size 6-dimensional array with (xx, xy, yy, xz, yz, zz) entries specifying the periodic cell
- * \return \f$| x - y |^2\f$
- */
-double Vector::PeriodicDistanceSquared(const Vector &y, const Matrix &cell_size) const
-{
-  double res = DistanceSquared(y), tmp;
-    Vector Shiftedy, TranslationVector;
-    int N[NDIM];
-
-    // 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]++)
-      for (N[1]=-1;N[1]<=1;N[1]++)
-        for (N[2]=-1;N[2]<=1;N[2]++) {
-          // create the translation vector
-          TranslationVector = cell_size * Vector(N[0],N[1],N[2]);
-          // add onto the original vector to compare with
-          Shiftedy = y + TranslationVector;
-          // get distance and compare with minimum so far
-          tmp = DistanceSquared(Shiftedy);
-          if (tmp < res) res = tmp;
-        }
-    return (res);
-};
 
 /** Calculates scalar product between this and another vector.

src/vector.hpp

@@ -42 +42 @@
   double DistanceSquared(const Vector &y) const;
   double DistanceToSpace(const Space& space) 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;