Changeset ed9da4 for src/Fragmentation

Timestamp:

Oct 26, 2012, 1:24:01 PM (12 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:

d4d7a1

Parents:

f7307f

git-author:

Frederik Heber <heber@…> (09/07/12 10:22:35)

git-committer:

Frederik Heber <heber@…> (10/26/12 13:24:01)

Message:

Replaced OrderArray and MaxArray arrays in Fragmentation::ParseOrderAtSiteFromFile().

• OrderArray is now a map, MaxArray uses AtomMask_t

Location:

src/Fragmentation

Files:

• Fragmentation.cpp (modified) (4 diffs)
• Mask.hpp (modified) (1 diff)

src/Fragmentation/Fragmentation.cpp

@@ -577 +577 @@
 bool Fragmentation::ParseOrderAtSiteFromFile(std::string &path)
 {
-  unsigned char *OrderArray = new unsigned char[mol->getAtomCount()];
-  bool *MaxArray = new bool[mol->getAtomCount()];
+  typedef unsigned char order_t;
+  typedef std::map<atomId_t, order_t> OrderArray_t;
+  OrderArray_t OrderArray;
+  AtomMask_t MaxArray;
   bool status;
   int AtomNr, value;
   string line;
   ifstream file;
-
-  for(int i=0;i<mol->getAtomCount();i++) {
-    OrderArray[i] = 0;
-    MaxArray[i] = false;
-  }
 
   LOG(1, "Begin of ParseOrderAtSiteFromFile");
@@ -600 +597 @@
         OrderArray[AtomNr] = value;
         file >> value;
-        MaxArray[AtomNr] = value;
+        MaxArray.setValue(AtomNr, (bool)value);
         //LOG(2, "AtomNr " << AtomNr << " with order " << (int)OrderArray[AtomNr] << " and max order set to " << (int)MaxArray[AtomNr] << ".");
       }
@@ -609 +606 @@
     for(molecule::iterator iter=mol->begin();iter!=mol->end();++iter){
       (*iter)->AdaptiveOrder = OrderArray[(*iter)->getNr()];
-      (*iter)->MaxOrder = MaxArray[(*iter)->getNr()];
+      (*iter)->MaxOrder = MaxArray.isTrue((*iter)->getNr());
     }
     //SetAtomValueToIndexedArray( OrderArray, &atom::getNr(), &atom::AdaptiveOrder );
@@ -620 +617 @@
     status = false;
   }
-  delete[](OrderArray);
-  delete[](MaxArray);
 
   LOG(1, "End of ParseOrderAtSiteFromFile");

src/Fragmentation/Mask.hpp

@@ -69 +69 @@
   }
 
+  /** Sets bit associated to \a id to a specific boolean value.
+   *
+   * @param id id to set or unset
+   * @param value bit giving whether to set or unset
+   */
+  void setValue(const T id, bool value) {
+    if (value)
+      setTrue(id);
+    else
+      setFalse(id);
+  }
+
   /** Use in printing the bit mask bit by bit.
    *