Changeset 29f7c1

Timestamp:

Feb 11, 2016, 8:07:50 AM (9 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:

951aa6

Parents:

c0f2fc

git-author:

Frederik Heber <heber@…> (12/29/15 19:49:43)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:07:50)

Message:

Molecule now has maps with old values for bond counts and element number per atom.

• this allows to update the total bond count and the formula in an O(N log N) fashion.

Location:

src

Files:

• molecule.cpp (modified) (7 diffs)
• molecule.hpp (modified) (3 diffs)

src/molecule.cpp

@@ -92 +92 @@
   ActiveFlag(false),
   IndexNr(-1),
-  NoNonHydrogen(this,boost::bind(&molecule::doCountNoNonHydrogen,this),"NoNonHydrogen"),
-  BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
+  NoNonHydrogen(0),
+  BondCount(0),
   atomIdPool(1, 20, 100),
   BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
@@ -153 +153 @@
 int molecule::getAtomCount() const{
   return atomIds.size();
-}
-
-size_t molecule::getNoNonHydrogen() const{
-  return *NoNonHydrogen;
-}
-
-int molecule::getBondCount() const{
-  return *BondCount;
 }
 
@@ -293 +285 @@
   }
   NOTIFY(FormulaChanged);
-  formula-=_atom->getType();
   _atom->removeFromMolecule();
   return iter;
@@ -330 +321 @@
     setAtomName(key);
     NOTIFY(FormulaChanged);
-    formula+=key->getType();
     return res;
   } else {
@@ -1172 +1162 @@
         OBSERVE;
         NOTIFY(FormulaChanged);
-        resetFormula();
+        const ElementPerAtom_t::iterator iter = ElementPerAtom.find(_lastchangedatomid);
+        ASSERT( iter != ElementPerAtom.end(),
+            "molecule::recieveNotification() - atom "
+            +toString(_atom->getId()+" is not contained in ElementsPerAtom."));
+        formula -= iter->second;
+        if (iter->second == (atomicNumber_t)1) // was a hydrogen ?
+          --NoNonHydrogen;
+        iter->second = _atom->getElementNo();
+        formula += iter->second;
+        if (iter->second == (atomicNumber_t)1) // is a hydrogen ?
+          ++NoNonHydrogen;
         break;
+      }
+      case AtomObservable::BondsAdded:
+      case AtomObservable::BondsRemoved:
+      {
+        // emit others about one of our atoms moved
+        _lastchangedatomid = _atom->getId();
+        const BondCountsPerAtom_t::iterator iter = BondCountsPerAtom.find(_lastchangedatomid);
+        ASSERT( iter != BondCountsPerAtom.end(),
+            "molecule::recieveNotification() - atom "
+            +toString(_atom->getId()+" is not contained in BondCountsPerAtom."));
+        BondCount -= iter->second;
+        iter->second = _atom->getListOfBonds().size();
+        BondCount += iter->second;
+       break;
       }
       default:
@@ -1216 +1230 @@
   _atom->signOn(this, AtomObservable::PositionChanged);
   _atom->signOn(this, AtomObservable::ElementChanged);
+  _atom->signOn(this, AtomObservable::BondsAdded);
+  _atom->signOn(this, AtomObservable::BondsRemoved);
   insert(_atom);
+  {
+    const size_t atom_bondcount = _atom->getListOfBonds().size();
+#ifndef NDEBUG
+    const std::pair<BondCountsPerAtom_t::iterator, bool> inserter =
+#endif
+    BondCountsPerAtom.insert( std::make_pair(_atom->getId(), atom_bondcount) );
+    ASSERT( inserter.second,
+       "molecule::associateAtomWithMolecule() - atom "
+        +toString(_atom->getId()+" already in BondCountsPerAtom."));
+    BondCount += atom_bondcount;
+  }
+  {
+    const int atom_elementno = _atom->getElementNo();
+#ifndef NDEBUG
+    const std::pair<ElementPerAtom_t::iterator, bool> inserter =
+#endif
+    ElementPerAtom.insert( std::make_pair(_atom->getId(), atom_elementno) );
+    ASSERT( inserter.second,
+       "molecule::associateAtomWithMolecule() - atom "
+        +toString(_atom->getId()+" already in ElementPerAtom."));
+    formula += atom_elementno;
+  }
 }
 
@@ -1223 +1261 @@
   _atom->signOff(this, AtomObservable::PositionChanged);
   _atom->signOff(this, AtomObservable::ElementChanged);
+  _atom->signOff(this, AtomObservable::BondsAdded);
+  _atom->signOff(this, AtomObservable::BondsRemoved);
   erase(_atom);
+  {
+    const BondCountsPerAtom_t::iterator iter = BondCountsPerAtom.find(_atom->getId());
+    ASSERT( iter != BondCountsPerAtom.end(),
+        "molecule::disassociateAtomWithMolecule() - atom "
+        +toString(_atom->getId()+" is not contained in BondCountsPerAtom."));
+    BondCount -= iter->second;
+    BondCountsPerAtom.erase(iter);
+  }
+  {
+    const ElementPerAtom_t::iterator iter = ElementPerAtom.find(_atom->getId());
+    ASSERT( iter != ElementPerAtom.end(),
+        "molecule::disassociateAtomWithMolecule() - atom "
+        +toString(_atom->getId()+" is not contained in ElementPerAtom."));
+    formula -= iter->second;
+    ElementPerAtom.erase(iter);
+  }
 }
 

src/molecule.hpp

@@ -94 +94 @@
 private:
   Formula formula;
-  Cacheable<size_t> NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
-  Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
+  size_t NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
+  int BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
   AtomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
@@ -136 +136 @@
   int getAtomCount() const;
   size_t doCountNoNonHydrogen() const;
-  size_t getNoNonHydrogen() const;
-  int getBondCount() const;
   int doCountBonds() const;
+  size_t getNoNonHydrogen() const{
+    return NoNonHydrogen;
+  }
+
+  int getBondCount() const{
+    return BondCount;
+  }
   moleculeId_t getId() const;
   void setId(moleculeId_t);
@@ -357 +362 @@
       > AtomDistanceMap_t;
   std::vector<AtomDistanceMap_t> BoundingBoxSweepingAxis;
+
+  //!> typedef for a map with current bond counts per atom
+  typedef std::map<atomId_t, size_t> BondCountsPerAtom_t;
+
+  //!> current bond counts per atom to update the BondCount
+  BondCountsPerAtom_t BondCountsPerAtom;
+
+  //!> typedef for a map with current element per atom
+  typedef std::map<atomId_t, atomicNumber_t> ElementPerAtom_t;
+
+  //!> current element per atom to update the BondCount
+  ElementPerAtom_t ElementPerAtom;
 
   //!> make setMolecule friend to access associateAtomWithMolecule()