Changeset b3d687 for src/Filling/Filler.cpp

Timestamp:

Apr 5, 2012, 3:57:16 PM (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:

5cdd83

Parents:

259887

git-author:

Frederik Heber <heber@…> (04/05/12 08:14:13)

git-committer:

Frederik Heber <heber@…> (04/05/12 15:57:16)

Message:

FIX: Filler::operator() did not create a molecule for each cloned cluster.

• so far we assume (in AtomicInfo) that each atoms always belongs to a molecule. However, the CopyAtomsInterface copies without creating new molecules or associating copied ones with the old molecules.
• AtomicInfo asserts that atom is associated to a molecule.
• CopyAtoms_withBonds now associates cloned atoms with molecule of original atom.
• Filler::operator() creates a molecule for each cloned cluster and associates all atoms in the cluster with it.
• This [closes #180].

File:

• src/Filling/Filler.cpp (modified) (3 diffs)

src/Filling/Filler.cpp

@@ -39 +39 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include "molecule.hpp"
 #include "NodeTypes.hpp"
 #include "Predicates/FillPredicate.hpp"
@@ -86 +87 @@
   NodeSet FillNodes(nodes.size(), zeroVec);
 
-  // move filler cluster's atoms out of domain such that it does not disturb the predicate.
-  // we only move the atoms as otherwise two translate ShapeOps will be on top of the Shape
-  // which is subsequently copied to all other cloned Clusters ...
-  Vector BoxDiagonal;
+  // evaluate predicates at each FillNode
   {
-    const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
-    BoxDiagonal = (M * Vector(1.,1.,1.));
-    BoxDiagonal -= cluster->getShape().getCenter();
-    BoxDiagonal *= 1. + 2.*cluster->getShape().getRadius()/BoxDiagonal.Norm(); // extend it a little further
-    AtomIdSet atoms = cluster->getAtoms();
-    for (AtomIdSet::iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
-      (*iter)->setPosition( (*iter)->getPosition() + BoxDiagonal );
-    LOG(1, "INFO: Translating original cluster's atoms by " << BoxDiagonal << ".");
-  }
+    // move filler cluster's atoms out of domain such that it does not disturb the predicate.
+    // we only move the atoms as otherwise two translate ShapeOps will be on top of the Shape
+    // which is subsequently copied to all other cloned Clusters ...
+    Vector BoxDiagonal;
+    {
+      const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
+      BoxDiagonal = (M * Vector(1.,1.,1.));
+      BoxDiagonal -= cluster->getShape().getCenter();
+      BoxDiagonal *= 1. + 2.*cluster->getShape().getRadius()/BoxDiagonal.Norm(); // extend it a little further
+      AtomIdSet atoms = cluster->getAtoms();
+      for (AtomIdSet::iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+        (*iter)->setPosition( (*iter)->getPosition() + BoxDiagonal );
+      LOG(1, "INFO: Translating original cluster's atoms by " << BoxDiagonal << ".");
+    }
 
-  // evaluate predicate and gather into new set
-  NodeSet::iterator transform_end  =
-      std::remove_copy_if(nodes.begin(), nodes.end(), FillNodes.begin(), predicate );
-  FillNodes.erase(transform_end, FillNodes.end());
+    // evaluate predicate and gather into new set
+    NodeSet::iterator transform_end  =
+        std::remove_copy_if(nodes.begin(), nodes.end(), FillNodes.begin(), predicate );
+    FillNodes.erase(transform_end, FillNodes.end());
 
-  // shift cluster back to original place
-  {
-    AtomIdSet atoms = cluster->getAtoms();
-    for (AtomIdSet::iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
-      (*iter)->setPosition( (*iter)->getPosition() - BoxDiagonal );
-    LOG(1, "INFO: Translating original cluster's atoms back.");
+    // shift cluster back to original place
+    {
+      AtomIdSet atoms = cluster->getAtoms();
+      for (AtomIdSet::iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+        (*iter)->setPosition( (*iter)->getPosition() - BoxDiagonal );
+      LOG(1, "INFO: Translating original cluster's atoms back.");
+    }
   }
 
@@ -123 +127 @@
   // clone clusters
   std::vector<ClusterInterface::Cluster_impl> clusters(FillNodes.size());
-  std::vector<ClusterInterface::Cluster_impl>::iterator clusteriter = clusters.begin();
-  *clusteriter = cluster;
-  clusteriter++;
-  std::generate_n(clusteriter, FillNodes.size()-1,
-      boost::bind(&ClusterInterface::clone, boost::cref(cluster), boost::ref(copyMethod), zeroVec) );
+  {
+    std::vector<ClusterInterface::Cluster_impl>::iterator clusteriter = clusters.begin();
+    *clusteriter = cluster;
+    clusteriter++;
+    std::generate_n(clusteriter, FillNodes.size()-1,
+        boost::bind(&ClusterInterface::clone, boost::cref(cluster), boost::ref(copyMethod), zeroVec) );
+  }
 
   // insert each cluster by abusing std::search a bit:
-  // we look for the subsequence of FillNodes inside clusters. If Inserter always
-  // returns true, we'll have the iterator pointing at first cluster
-  std::vector<ClusterInterface::Cluster_impl>::const_iterator inserteriter =
-    std::search(clusters.begin(), clusters.end(), FillNodes.begin(), FillNodes.end(),
-        boost::bind(&Inserter::operator(), boost::cref(inserter), _1, _2));
-  if( inserteriter != clusters.begin()) {
-    ELOG(1, "Not all cloned clusters could be successfully inserted.");
-    return false;
+  {
+    // we look for the subsequence of FillNodes inside clusters. If Inserter always
+    // returns true, we'll have the iterator pointing at first cluster
+    std::vector<ClusterInterface::Cluster_impl>::const_iterator inserteriter =
+      std::search(clusters.begin(), clusters.end(), FillNodes.begin(), FillNodes.end(),
+          boost::bind(&Inserter::operator(), boost::cref(inserter), _1, _2));
+    if( inserteriter != clusters.begin()) {
+      ELOG(1, "Not all cloned clusters could be successfully inserted.");
+      return false;
+    }
+  }
+
+  // create molecules for each cluster and fill in atoms
+  {
+    std::vector<molecule *> molecules(clusters.size()-1, NULL);
+    std::generate_n(molecules.begin(), FillNodes.size()-1,
+        boost::bind(&World::createMolecule, World::getPointer()) );
+    std::vector<ClusterInterface::Cluster_impl>::const_iterator clusteriter = clusters.begin();
+    ++clusteriter;
+    std::vector<molecule *>::iterator moliter = molecules.begin();
+    for (;moliter != molecules.end(); ++clusteriter, ++moliter) {
+      AtomIdSet atoms = (*clusteriter)->getAtoms();
+      for (AtomIdSet::iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+        (*moliter)->AddAtom(*iter);
+    }
   }