Changeset 7ac4af

Timestamp:

Jul 2, 2010, 9:36:29 AM (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:

5ec8e3

Parents:

a630fd

Message:

Added an optimized version of the Box::explode() method for n=1

Location:

src

Files:

• Box.cpp (modified) (2 diffs)
• Box.hpp (modified) (1 diff)

src/Box.cpp

@@ -81 +81 @@
   int max_dim2 = max_dim*max_dim;
   int max = max_dim2*max_dim;
+  // only one loop to avoid unneccessary jumps
   for(int i = 0;i<max;++i){
     // get all coordinates for this iteration
@@ -88 +89 @@
     Vector translation = translateIn(Vector(n1,n2,n3));
     res.push_back(translation);
+  }
+  // translate all the translation vector by the offset defined by point
+  res.translate(point);
+  return res;
+}
+
+VECTORSET(std::list) Box::explode(const Vector &point) const{
+  VECTORSET(std::list) res;
+
+  // translate the Vector into each of the 27 neighbourhoods
+
+  // first create all 27 translation Vectors
+  // these loops depend on fixed parameters and can easily be expanded
+  // by the compiler to allow code without jumps
+  for(int n1 = -1;n1<=1;++n1){
+    for(int n2 = -1;n2<=1;++n2){
+      for(int n3 = -1;n3<=1;++n3){
+        // get all coordinates for this iteration
+        Vector translation = translateIn(Vector(n1,n2,n3));
+        res.push_back(translation);
+      }
+    }
   }
   // translate all the translation vector by the offset defined by point

src/Box.hpp

@@ -69 +69 @@
    * Carefull, needs O(n^3) time and produces as many vectors.
    */
-  VECTORSET(std::list) explode(const Vector &point,int n=1) const;
+  VECTORSET(std::list) explode(const Vector &point,int n) const;
+  VECTORSET(std::list) explode(const Vector &point) const;
 
   /**