Changeset 7f3b9d for src/moleculelist.cpp

Timestamp:

May 23, 2008, 9:17:19 AM (18 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, Candidate_v1.7.0, 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:

040f93

Parents:

6097ea

Message:

Lots of for loops now count in reverse order where it does not matter, some 3 -> NDIM

for(i=0;i<var;i++) is slower than for (i=var;i--;) if the order of the i's is not important (note: i-- is also a value and it stops when on i == 0 automatically)
in builder.cpp there were some remnant 3 actually meant to be NDIM

File:

• src/moleculelist.cpp (modified) (8 diffs)

src/moleculelist.cpp

@@ -22 +22 @@
 {
   ListOfMolecules = (molecule **) Malloc(sizeof(molecule *)*NumMolecules, "MoleculeListClass:MoleculeListClass: **ListOfMolecules");
-  for (int i=0;i<NumMolecules;i++)
+  for (int i=NumMolecules;i--;)
     ListOfMolecules[i] = NULL;
   NumberOfMolecules = NumMolecules;
@@ -34 +34 @@
 {
   cout << Verbose(3) << this << ": Freeing ListOfMolcules." << endl;
-  for (int i=0;i<NumberOfMolecules;i++) {
+  for (int i=NumberOfMolecules;i--;) {
     if (ListOfMolecules[i] != NULL) { // if NULL don't free
       cout << Verbose(4) << "ListOfMolecules: Freeing " << ListOfMolecules[i] << "." << endl;
@@ -66 +66 @@
     else {
       Count = (**(molecule **)a).AtomCount;
-      aList = (int *) Malloc(sizeof(int)*Count, "MolCompare: *aList");
-      bList = (int *) Malloc(sizeof(int)*Count, "MolCompare: *bList");
+      aList = new int[Count];
+      bList = new int[Count];
   
       // fill the lists
@@ -114 +114 @@
         }
       }
-      Free((void **)&aList, "MolCompare: *aList");
-      Free((void **)&bList, "MolCompare: *bList");
+      delete[](aList);
+      delete[](bList);
       return flag;
     }
@@ -244 +244 @@
     ListOfMolecules[i]->SetBoxDimension(&BoxDimension);  // update Box of atoms by boundary
     int j = -1;
-    for (int k=0;k<3;k++) {
+    for (int k=0;k<NDIM;k++) {
       j += k+1;
       BoxDimension.x[k] = 5.;
@@ -268 +268 @@
     outputFragment.close();
     outputFragment.clear();
-    Free((void **)&FragmentNumber, "MoleculeListClass::OutputConfigForListOfFragments: *FragmentNumber");
+    delete(FragmentNumber);
+    //Free((void **)&FragmentNumber, "MoleculeListClass::OutputConfigForListOfFragments: *FragmentNumber");
   }
   cout << " done." << endl;
@@ -461 +462 @@
     ListOfLocalAtoms = (atom ***) Malloc(sizeof(atom **)*Counter, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
     if (ListOfLocalAtoms != NULL) {
-      for (int i=0;i<Counter;i++)
+      for (int i=Counter;i--;)
         ListOfLocalAtoms[i] = NULL;
       FreeList = FreeList && true;
@@ -501 +502 @@
     KeySetCounter = Count();
     FragmentList = (Graph **) Malloc(sizeof(Graph *)*KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
-    for(int i=0;i<KeySetCounter;i++)
+    for(int i=KeySetCounter;i--;)
       FragmentList[i] = NULL;
     KeySetCounter = 0;