Changeset c6ab91 for src

Timestamp:

Apr 14, 2013, 6:35:27 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:

78ca37

Parents:

356ae4

git-author:

Frederik Heber <heber@…> (03/04/13 17:40:55)

git-committer:

Frederik Heber <heber@…> (04/14/13 18:35:27)

Message:

Wrote faster molecule::FindAtom().

• due to local id nature in Fragmentation many functions there make heavy use of this function. However, has it scales linearly, this severly limits the abilitiy to tackle large molecules.
• as quick short-cut we installed a map from local to global ids, updated by insert() and erase() and used by FindAtom().

Location:

src

Files:

• molecule.cpp (modified) (7 diffs)
• molecule.hpp (modified) (2 diffs)

src/molecule.cpp

@@ -132 +132 @@
 }
 
+void molecule::InsertLocalToGlobalId(atom * const pointer)
+{
+#ifndef NDEBUG
+  std::pair< LocalToGlobalId_t::iterator, bool > inserter =
+#endif
+      LocalToGlobalId.insert( std::make_pair(pointer->getNr(), pointer) );
+  ASSERT( inserter.second,
+      "molecule::AddAtom() - local number "+toString(pointer->getNr())+" appears twice.");
+}
+
 bool molecule::changeAtomNr(int oldNr, int newNr, atom* target){
   OBSERVE;
@@ -138 +148 @@
     if (oldNr != -1)  // -1 is reserved and indicates no number
       atomIdPool.releaseId(oldNr);
+    LocalToGlobalId.erase(oldNr);
     ASSERT (target,
         "molecule::changeAtomNr() - given target is NULL, cannot set Nr or name.");
     target->setNr(newNr);
+    InsertLocalToGlobalId(target);
     setAtomName(target);
     return true;
@@ -202 +214 @@
     NOTIFY(AtomNrChanged);
     atomIdPool.releaseId(_atom->getNr());
+    LocalToGlobalId.erase(_atom->getNr());
     _atom->setNr(-1);
   }
@@ -220 +233 @@
       NOTIFY(AtomNrChanged);
       atomIdPool.releaseId(key->getNr());
+      LocalToGlobalId.erase(key->getNr());
       key->setNr(-1);
     }
@@ -236 +250 @@
     NOTIFY(AtomNrChanged);
     key->setNr(atomIdPool.getNextId());
+    InsertLocalToGlobalId(key);
     setAtomName(key);
     formula+=key->getType();
@@ -283 +298 @@
   if (pointer != NULL) {
     atom *walker = pointer->clone();
-    walker->setName(pointer->getName());
-    walker->setNr(last_atom++);  // increase number within molecule
-    insert(walker);
-    walker->setMolecule(this);
+    AddAtom(walker);
     retval=walker;
   }
@@ -777 +789 @@
 atom * molecule::FindAtom(int Nr)  const
 {
-  molecule::iterator iter = begin();
-  for (; iter != end(); ++iter)
-  if ((*iter)->getNr() == Nr)
-    break;
-  if (iter != end()) {
+  LocalToGlobalId_t::const_iterator iter = LocalToGlobalId.find(Nr);
+  if (iter != LocalToGlobalId.end()) {
     //LOG(0, "Found Atom Nr. " << walker->getNr());
-    return (*iter);
+    return iter->second;
   } else {
     ELOG(1, "Atom with Nr " << Nr << " not found in molecule " << getName() << "'s list.");

src/molecule.hpp

@@ -88 +88 @@
   AtomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
   IdPool<atomId_t, uniqueId> atomIdPool;  //!< pool of internal ids such that way may guarantee uniqueness
+  typedef std::map<atomId_t,atom *> LocalToGlobalId_t;
+  LocalToGlobalId_t LocalToGlobalId; //!< internal map to ease FindAtom
 
 protected:
@@ -220 +222 @@
    */
   bool changeAtomNr(int oldNr, int newNr, atom* target=0);
+
+  /** Updates the internal lookup fro local to global indices.
+   *
+   * \param pointer pointer to atom
+   */
+  void InsertLocalToGlobalId(atom * const pointer);
 
   /** Sets the name of the atom.