Changeset 3738f0 for src/bondgraph.cpp

Timestamp:

Mar 1, 2011, 12:49:28 PM (15 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, Candidate_v1.7.0, 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:

0cbad2

Parents:

ce5f05

git-author:

Frederik Heber <heber@…> (02/26/11 00:10:05)

git-committer:

Frederik Heber <heber@…> (03/01/11 12:49:28)

Message:

Moved molecule::CreateAdjacencyList over to class BondGraph.

to make this possible we had to:

• enhance AtomSet such that individual const_ and iterator are templated.
• FIX: FragmentationCreateAdjacencyAction needs to call BondGraph::SetMaxDistanceToMaxOfCovalentRadii() before getMaxDistance() is valid.
• new function molecule::getAtomSet() which copies the internal atomSet to a vector AtomSetMixin and delivers. This is needed as PointCloudAdaptor needs a reference to a AtomSetMixin and we don't want to expose the internal set.

other changes:

• the following Actions do not create adjacency beforehand anymore:
  • DepthFirstSearchAction
  • MoleculeSaveAdjacencyAction
  • MoleculeSaveBondsAction
• changes to BondGraph:
  • removed CreateAdjacencyForMolecule()
  • removed SetMaxDistanceToMaxOfCovalentRadii()
  • new function CreateAdjacency on LinkedCell reference
• new BondGraph functions that work on AtomSetMixin reference: CreateAdjacency(), cleanAdjacencyList(), CorrectBondDegree(), resetBondDegree(), calculateBondDegree()

TESTFIXES:

• the regression test for all Actions mentioned above that don't create adjacency themselves anymore needed to be prepended with --select-all-atoms --create-adjacency.

File:

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

src/bondgraph.cpp

@@ -25 +25 @@
 #include "bond.hpp"
 #include "bondgraph.hpp"
+#include "Box.hpp"
 #include "element.hpp"
 #include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Range.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
 #include "parser.hpp"
 #include "periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include "World.hpp"
+#include "WorldTime.hpp"
 
 const double BondGraph::BondThreshold = 0.4;   //!< CSD threshold in bond check which is the width of the interval whose center is the sum of the covalent radii
@@ -40 +44 @@
     max_distance(0),
     IsAngstroem(IsA)
-{};
+{}
 
 BondGraph::~BondGraph()
@@ -47 +51 @@
     delete(BondLengthMatrix);
   }
-};
+}
 
 bool BondGraph::LoadBondLengthTable(std::istream &input)
@@ -57 +61 @@
   // allocate MatrixContainer
   if (BondLengthMatrix != NULL) {
-    DoLog(1) && (Log() << Verbose(1) << "MatrixContainer for Bond length already present, removing." << endl);
+    LOG(1, "MatrixContainer for Bond length already present, removing.");
     delete(BondLengthMatrix);
   }
@@ -64 +68 @@
   // parse in matrix
   if ((input.good()) && (status = TempContainer->ParseMatrix(input, 0, 1, 0))) {
-    DoLog(1) && (Log() << Verbose(1) << "Parsing bond length matrix successful." << endl);
+    LOG(1, "Parsing bond length matrix successful.");
   } else {
     DoeLog(1) && (eLog()<< Verbose(1) << "Parsing bond length matrix failed." << endl);
@@ -87 +91 @@
   }
   return status;
-};
-
-bool BondGraph::CreateAdjacencyForMolecule(molecule * const mol)
-{
-  Info FunctionInfo(__func__);
-  bool status = true;
-
-  if (mol->empty()) // only construct if molecule is not empty
-    return false;
-
-  SetMaxDistanceToMaxOfCovalentRadii(mol);
-  mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::getMinMaxDistance, this);
-
-  return status;
-};
+}
 
 double BondGraph::GetBondLength(int firstZ, int secondZ)
@@ -113 +103 @@
     return (BondLengthMatrix->Matrix[0][firstZ][secondZ]);
   }
-};
-
-double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol)
-{
-  Info FunctionInfo(__func__);
-  max_distance = 0.;
-
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    if ((*iter)->getType()->getCovalentRadius() > max_distance)
-      max_distance = (*iter)->getType()->getCovalentRadius();
-  }
-  max_distance *= 2.;
-  max_distance += BondThreshold;
-
-  return max_distance;
-};
+}
 
 double BondGraph::getMaxDistance() const
@@ -142 +117 @@
   MaxDistance = MinDistance + BondThreshold;
   MinDistance -= BondThreshold;
-};
+}
 
 void BondGraph::BondLengthMatrixMinMaxDistance(const BondedParticle * const Walker, const BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
@@ -152 +127 @@
   MaxDistance = MinDistance + BondThreshold;
   MinDistance -= BondThreshold;
-};
+}
 
 void BondGraph::getMinMaxDistance(const BondedParticle * const Walker, const BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
@@ -164 +139 @@
   }
 }
+
+void BondGraph::CreateAdjacency(LinkedCell &LC)
+{
+  atom *Walker = NULL;
+  atom *OtherWalker = NULL;
+  int n[NDIM];
+  double MinDistance, MaxDistance;
+  Box &domain = World::getInstance().getDomain();
+
+  unsigned int BondCount = 0;
+  // 3a. go through every cell
+  LOG(3, "INFO: Celling ... ");
+  for (LC.n[0] = 0; LC.n[0] < LC.N[0]; LC.n[0]++)
+    for (LC.n[1] = 0; LC.n[1] < LC.N[1]; LC.n[1]++)
+      for (LC.n[2] = 0; LC.n[2] < LC.N[2]; LC.n[2]++) {
+        const TesselPointSTLList *List = LC.GetCurrentCell();
+        LOG(2, "Current cell is " << LC.n[0] << ", " << LC.n[1] << ", " << LC.n[2] << " with No. " << LC.index << " containing " << List->size() << " points.");
+        if (List != NULL) {
+          for (TesselPointSTLList::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
+            Walker = dynamic_cast<atom*>(*Runner);
+            ASSERT(Walker != NULL,
+                "BondGraph::CreateAdjacency() - Tesselpoint that was not an atom retrieved from LinkedNode");
+            LOG(2, "INFO: Current Atom is " << *Walker << ".");
+            // 3c. check for possible bond between each atom in this and every one in the 27 cells
+            for (n[0] = -1; n[0] <= 1; n[0]++)
+              for (n[1] = -1; n[1] <= 1; n[1]++)
+                for (n[2] = -1; n[2] <= 1; n[2]++) {
+                  const TesselPointSTLList *OtherList = LC.GetRelativeToCurrentCell(n);
+                  if (OtherList != NULL) {
+                    LOG(3, "INFO: Current relative cell is " << LC.n[0] << ", " << LC.n[1] << ", " << LC.n[2] << " with No. " << LC.index << " containing " << List->size() << " points.");
+                    for (TesselPointSTLList::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
+                      if ((*OtherRunner) > Walker) {  // just to not add bonds from both sides
+                        OtherWalker = dynamic_cast<atom*>(*OtherRunner);
+                        ASSERT(OtherWalker != NULL,
+                            "BondGraph::CreateAdjacency() - TesselPoint that was not an atom retrieved from LinkedNode");
+                        getMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+                        const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
+                        LOG(2, "INFO: Checking distance " << distance << " against typical bond length of [" << MinDistance * MinDistance << "," << MaxDistance * MaxDistance << "].");
+                        const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
+                        LOG(3, "INFO: MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << ".");
+                        if (OtherWalker->father > Walker->father ) { // just to not add bonds from both sides
+                          if (status) { // create bond if distance is smaller
+                            LOG(1, "ACCEPT: Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << ".");
+                            bond * Binder = new bond(Walker->father, OtherWalker->father, 1);
+                            Walker->father->RegisterBond(WorldTime::getTime(), Binder);
+                            OtherWalker->father->RegisterBond(WorldTime::getTime(), Binder);
+                            BondCount++;
+                          } else {
+                            LOG(1, "REJECT: Squared distance "
+                                << distance << " is out of covalent bounds ["
+                                << MinDistance*MinDistance << ","
+                                << MaxDistance * MaxDistance << "].");
+                          }
+                        } else {
+                          LOG(5, "REJECT: Not Adding: Wrong order of father's.");
+                        }
+                      } else {
+                        LOG(5, "REJECT: Not Adding: Wrong order.");
+                      }
+                    }
+                  }
+                }
+          }
+        }
+      }
+    LOG(1, "I detected " << BondCount << " bonds in the molecule.");
+}