Changeset e39e7a for src/molecule.cpp

Timestamp:

Jan 31, 2016, 12:43:17 PM (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:

6a922b

Parents:

e3e52a

git-author:

Frederik Heber <heber@…> (08/31/15 12:38:50)

git-committer:

Frederik Heber <heber@…> (01/31/16 12:43:17)

Message:

Implemented more efficient per-molecule bounding box information.

• molecule now has internal bimaps to know the extent of itself in a cheap way, right map needs to be multiset_of to allow for non-unique values.
• moved BoundingBoxInfo from GLMolObject to molecule.
• is itself a Cacheable and is requested from GLMoleculeObject_molecule on new channel BoundingBoxChanged.
• Cacheable listens to AtomInserted, AtomRemoved, and AtomMoved.
• in molecule::changeAtomId() we also change BoundingBoxSweepingAxis entry.

File:

• src/molecule.cpp (modified) (10 diffs)

src/molecule.cpp

@@ -36 +36 @@
 
 #include <algorithm>
+#include <boost/assign.hpp>
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
@@ -50 +51 @@
 #include "CodePatterns/enumeration.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Observer/Observable.hpp"
 #include "CodePatterns/Observer/Notification.hpp"
 #include "config.hpp"
@@ -67 +69 @@
 #include "WorldTime.hpp"
 
+using namespace boost::assign;
+
+// static entities
+static Observable::channels_t getBoundingBoxChannels()
+{
+  Observable::channels_t channels;
+  channels += molecule::AtomInserted, molecule::AtomRemoved, molecule::AtomMoved;
+  return channels;
+}
 
 /************************************* Functions for class molecule *********************************/
@@ -83 +94 @@
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
   atomIdPool(1, 20, 100),
+  BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
   _lastchangedatomid(-1),
   last_atom(0)
@@ -92 +104 @@
     OurChannel->addChannel(type);
 
+  // cannot initialize in initializer body as then channels have not been setup yet
+  BoundingBox.reset(
+      new Cacheable<BoundingBoxInfo>(
+          this, boost::bind(&molecule::updateBoundingBox, boost::cref(this)), "molecule_BoundingBox", getBoundingBoxChannels()));
+
   strcpy(name,World::getInstance().getDefaultName().c_str());
-};
+}
 
 molecule *NewMolecule(){
@@ -177 +194 @@
   atomIds.erase( oldId );
   atomIds.insert( newId );
+  // also update BoundingBoxSweepingAxis
+  for (int i=0;i<NDIM;++i) {
+    AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(oldId);
+    ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
+        "molecule::changeAtomId() - could not find atom "+toString(oldId)
+        +" in BoundingBoxSweepingAxis.");
+    const double component = iter->second;
+    BoundingBoxSweepingAxis[i].left.erase(iter);
+    BoundingBoxSweepingAxis[i].left.insert( std::make_pair(newId, component) );
+  }
   return true;
 }
@@ -237 +264 @@
   atomIds.erase( _atom->getId() );
   {
+    BoundingBoxInfo oldinfo = updateBoundingBox();
+    for (int i=0;i<NDIM;++i)
+      BoundingBoxSweepingAxis[i].left.erase( _atom->getId() );
+    BoundingBoxInfo newinfo = updateBoundingBox();
+    if (oldinfo != newinfo)
+      NOTIFY(BoundingBoxChanged);
+  }
+  {
     NOTIFY(AtomNrChanged);
     atomIdPool.releaseId(_atom->getNr());
@@ -264 +299 @@
   std::pair<iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
+    {
+      BoundingBoxInfo oldinfo = updateBoundingBox();
+      for (int i=0;i<NDIM;++i)
+        BoundingBoxSweepingAxis[i].left.insert( std::make_pair(key->getId(), key->getPosition()[i]));
+      BoundingBoxInfo newinfo = updateBoundingBox();
+      if (oldinfo != newinfo)
+        NOTIFY(BoundingBoxChanged);
+    }
     NOTIFY(AtomNrChanged);
     key->setNr(atomIdPool.getNextId());
@@ -1033 +1076 @@
 }
 
+molecule::BoundingBoxInfo molecule::updateBoundingBox() const
+{
+  BoundingBoxInfo info;
+  Vector min = zeroVec;
+  Vector max = zeroVec;
+  for (int i=0;i<NDIM;++i) {
+    if (!BoundingBoxSweepingAxis[i].right.empty()) {
+      min[i] = BoundingBoxSweepingAxis[i].right.begin()->first;
+      max[i] = BoundingBoxSweepingAxis[i].right.rbegin()->first;
+    }
+  }
+  info.radius = (.5*(max-min)).Norm();
+  info.position = .5*(max+min);
+  return info;
+}
+
+molecule::BoundingBoxInfo molecule::getBoundingBox() const
+{
+  return **BoundingBox;
+}
+
 void molecule::update(Observable *publisher)
 {
@@ -1052 +1116 @@
         // emit others about one of our atoms moved
         _lastchangedatomid = _atom->getId();
+        // update entry in map
+        BoundingBoxInfo oldinfo = updateBoundingBox();
+        for (int i=0;i<NDIM;++i) {
+          AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(_atom->getId());
+          ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
+              "molecule::recieveNotification() - could not find atom "+toString(_atom->getId())
+              +" in BoundingBoxSweepingAxis.");
+          BoundingBoxSweepingAxis[i].left.erase(iter);
+          BoundingBoxSweepingAxis[i].left.insert(
+              std::make_pair(_atom->getId(), _atom->getPosition()[i]) );
+        }
+        BoundingBoxInfo newinfo = updateBoundingBox();
         OBSERVE;
         NOTIFY(AtomMoved);
+        if (oldinfo != newinfo)
+          NOTIFY(BoundingBoxChanged);
         break;
       }