Changeset e791dc

Timestamp:

Apr 3, 2012, 8:00:19 AM (13 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:

2a3124

Parents:

108968

git-author:

Frederik Heber <heber@…> (03/13/12 17:52:00)

git-committer:

Frederik Heber <heber@…> (04/03/12 08:00:19)

Message:

Removed molecule::doCountAtom() and added molecule::doCountNoNonHydrogen().

• since the conversion of molecule to being a container for a set of atomicId_t counting atoms is just an unnecessary O(N^{2), since we count through all of them. With atomIds.size() however the number of atoms is always known.}
• Hence, moleucle::AtomCount is no longer a Cacheable, but NoNoHydrogen is now such a one. LazyEvaluation is only sensible when the evaluations are few. Due to updates from the GUI however, atomcount is constantly requested.
• FIX: removed doCountAtom() calls in some functions in analysis_correlation.

Location:

src

Files:

• Analysis/analysis_correlation.cpp (modified) (5 diffs)
• Fragmentation/Fragmentation.cpp (modified) (1 diff)
• molecule.cpp (modified) (5 diffs)
• molecule.hpp (modified) (3 diffs)

src/Analysis/analysis_correlation.cpp

@@ -295 +295 @@
   Info FunctionInfo(__func__);
   PairCorrelationMap *outmap = new PairCorrelationMap;
-  double distance = 0.;
+  //double distance = 0.;
   Box &domain = World::getInstance().getDomain();
 
@@ -391 +391 @@
     return outmap;
   }
-  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++)
-    (*MolWalker)->doCountAtoms();
+
   outmap = new CorrelationToPointMap;
   for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++) {
@@ -437 +436 @@
     return outmap;
   }
-  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++)
-    (*MolWalker)->doCountAtoms();
+
   outmap = new CorrelationToPointMap;
   for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++) {
@@ -492 +490 @@
     return outmap;
   }
-  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++)
-    (*MolWalker)->doCountAtoms();
+
   outmap = new CorrelationToSurfaceMap;
   for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++) {
@@ -549 +546 @@
     return outmap;
   }
-  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++)
-    (*MolWalker)->doCountAtoms();
+
   outmap = new CorrelationToSurfaceMap;
   double ShortestDistance = 0.;

src/Fragmentation/Fragmentation.cpp

@@ -456 +456 @@
     c = (ListOfBonds.size() > c) ? ListOfBonds.size() : c;
   }
-  FragmentCount = mol->NoNonHydrogen*(1 << (c*order));
-  LOG(1, "Upper limit for this subgraph is " << FragmentCount << " for " << mol->NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << ".");
+  FragmentCount = mol->getNoNonHydrogen()*(1 << (c*order));
+  LOG(1, "Upper limit for this subgraph is " << FragmentCount << " for "
+      << mol->getNoNonHydrogen() << " non-H atoms with maximum bond degree of " << c << ".");
   return FragmentCount;
 };

src/molecule.cpp

@@ -58 +58 @@
   Observable("molecule"),
   MDSteps(0),
-  NoNonHydrogen(0),
   NoNonBonds(0),
   NoCyclicBonds(0),
   ActiveFlag(false),
   IndexNr(-1),
-  AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"),
+  NoNonHydrogen(this,boost::bind(&molecule::doCountNoNonHydrogen,this),"NoNonHydrogen"),
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
   atomIdPool(1, 20, 100),
@@ -95 +94 @@
 
 int molecule::getAtomCount() const{
-  return *AtomCount;
+  return atomIds.size();
+}
+
+size_t molecule::getNoNonHydrogen() const{
+  return *NoNonHydrogen;
 }
 
@@ -236 +239 @@
   OBSERVE;
   if (pointer != NULL) {
-    if (pointer->getType()->getAtomicNumber() != 1)
-      NoNonHydrogen++;
     insert(pointer);
     pointer->setMolecule(this);
@@ -258 +259 @@
     walker->setNr(last_atom++);  // increase number within molecule
     insert(walker);
-    if ((pointer->getType() != NULL) && (pointer->getType()->getAtomicNumber() != 1))
-      NoNonHydrogen++;
     walker->setMolecule(this);
     retval=walker;
@@ -951 +950 @@
  * \param *out output stream for debugging
  */
-int molecule::doCountAtoms()
-{
-  int res = size();
-  NoNonHydrogen = 0;
+size_t molecule::doCountNoNonHydrogen() const
+{
+  int temp = 0;
   // go through atoms and look for new ones
   for (molecule::const_iterator iter = begin(); iter != end(); ++iter)
     if ((*iter)->getType()->getAtomicNumber() != 1) // count non-hydrogen atoms whilst at it
-      NoNonHydrogen++;
-  return res;
+      ++temp;
+  return temp;
 };
 

src/molecule.hpp

@@ -74 +74 @@
 
   int MDSteps; //!< The number of MD steps in Trajectories
-  mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
   mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
   mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
@@ -83 +82 @@
 private:
   Formula formula;
-  Cacheable<int> AtomCount; //!< number of atoms, brought up-to-date by doCountAtoms()
+  Cacheable<size_t> NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
   Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
@@ -98 +97 @@
   const std::string getName() const;
   int getAtomCount() const;
-  int doCountAtoms();
+  size_t doCountNoNonHydrogen() const;
+  size_t getNoNonHydrogen() const;
   int getBondCount() const;
   int doCountBonds() const;