Changeset 025048

Timestamp:

Oct 20, 2011, 12:39:01 PM (13 years ago)

Author:

Frederik Heber <heber@…>

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:

9317be

Parents:

93d78e8

Message:

Enhanced Box::periodicDistanceSquared() by an internal_explode().

• internal_explode() works on an static internal VECTORSET(list) such that there is no need for repeated memory allocation/deallocation for said list.

Location:

src

Files:

• Box.cpp (modified) (7 diffs)
• Box.hpp (modified) (1 diff)

src/Box.cpp

@@ -38 +38 @@
 
 using namespace std;
+
+VECTORSET(std::list) Box::internal_list;
 
 Box::Box() :
@@ -135 +137 @@
 VECTORSET(std::list) Box::explode(const Vector &point,int n) const{
   ASSERT(isInside(point),"Exploded point not inside Box");
-  VECTORSET(std::list) res;
+  internal_explode(point, n);
+  VECTORSET(std::list) res(internal_list);
+  return res;
+}
+
+void Box::internal_explode(const Vector &point,int n) const{
+  internal_list.clear();
 
   Vector translater = translateOut(point);
@@ -156 +164 @@
   if(!dims){
     // all boundaries are ignored
-    res.push_back(point);
-    return res;
+    internal_list.push_back(point);
+    return;
   }
 
@@ -189 +197 @@
         case Ignore:
           ASSERT(0,"Ignored coordinate handled in generation loop");
+          break;
         default:
           ASSERT(0,"No default case for this switch-case");
+          break;
       }
 
@@ -196 +206 @@
     // add back all ignored coordinates (not handled in above loop)
     helper+=mask;
-    res.push_back(translateIn(helper));
+    internal_list.push_back(translateIn(helper));
     // set the new indexes
     int pos=0;
@@ -209 +219 @@
     }
   }
-  return res;
 }
 
@@ -218 +227 @@
 
 double Box::periodicDistanceSquared(const Vector &point1,const Vector &point2) const{
-  Vector helper1 = WrapPeriodically(point1);
-  Vector helper2 = WrapPeriodically(point2);
-  VECTORSET(std::list) expansion = explode(helper1);
-  double res = expansion.minDistSquared(helper2);
+  Vector helper1(!isInside(point1) ? WrapPeriodically(point1) : point1);
+  Vector helper2(!isInside(point2) ? WrapPeriodically(point2) : point2);
+  internal_explode(helper1,1);
+  double res = internal_list.minDistSquared(helper2);
   return res;
 }

src/Box.hpp

@@ -122 +122 @@
 
 private:
+  /** Internal explode function that works on the staticly present internal_list
+   *
+   * \todo Note that is not thread-safe!
+   *
+   * Most of the time of explode is consumed by memory allocation if it is called
+   * repeatedly.
+   *
+   * @param point point to explode
+   * @param n neighbour shells to explode
+   */
+  void internal_explode(const Vector &point,int n) const;
+
+  //!> Internal vector list for exploding vectors and checking.
+  static VECTORSET(std::list) internal_list;
+
   Conditions_t conditions;
   RealSpaceMatrix *M;    //!< Defines the layout of the box