Changeset b70721

Timestamp:

Oct 30, 2009, 9:05:30 AM (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, 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:

b21a64

Parents:

46ea3b

git-author:

Frederik Heber <heber@…> (10/30/09 08:30:57)

git-committer:

Frederik Heber <heber@…> (10/30/09 09:05:30)

Message:

New class BondGraph.

• BondGraph parses a file containing bond lengths and basically has a member function which gives lower and upper bounds on when two atoms are bonded and when not.
  • BondGraph::LoadBondLengthTable() - basically uses MatrixContainer::ParseMatrix()
  • BondGraph::ConstructBondGraph() - uses molecule::CreateAdjacency() but with different bounds-function.
  • BondGraph::GetBondLength() - returns entry from parsed bond length matrix
  • BondGraph::CovalentMinMaxDistance() - bounds function using covalent radii of involved elements
  • BondGraph::BondLengthMatrixMinMaxDistance() - bounds function which uses the parsed bond length matrix
• Unit test written for BondGraph.
• molecule::CreateAdjacencyList() - rewritten, takes now a bounds BondGraph member function, if NULL is given, creates its own BondGraph and uses standard covalent bounds function (which does not need any scanning).
• new function BondedParticle::IsBondedTo() which checks whether given BondedPasrticle is contained in ListOfBonds.
• builder.cpp: calls to molecule::CreateAdjacencyList() adapted to new syntax.

Location:

src

Files:

• Makefile.am (modified) (1 diff)
• atom_bondedparticle.cpp (modified) (1 diff)
• atom_bondedparticle.hpp (modified) (1 diff)
• bondgraph.cpp (added)
• bondgraph.hpp (added)
• builder.cpp (modified) (5 diffs)
• molecule.hpp (modified) (2 diffs)
• molecule_graph.cpp (modified) (4 diffs)
• unittests/Makefile.am (modified) (1 diff)
• unittests/bondgraphunittest.cpp (added)
• unittests/bondgraphunittest.hpp (added)

src/Makefile.am

@@ -2 +2 @@
 ATOMHEADER = atom.hpp atom_atominfo.hpp atom_bondedparticle.hpp atom_bondedparticleinfo.hpp atom_graphnode.hpp atom_graphnodeinfo.hpp atom_particleinfo.hpp atom_trajectoryparticle.hpp atom_trajectoryparticleinfo.hpp
 
-SOURCE = analysis_correlation.cpp ${ATOMSOURCE} bond.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
-HEADER = analysis_correlation.hpp ${ATOMHEADER} bond.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
+SOURCE = analysis_correlation.cpp ${ATOMSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
+HEADER = analysis_correlation.hpp ${ATOMHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
 
 BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)

src/atom_bondedparticle.cpp

@@ -151 +151 @@
 };
 
+/** Checks whether there is a bond between \a this atom and the given \a *BondPartner.
+ * \param *BondPartner atom to check for
+ * \return true - bond exists, false - bond does not exist
+ */
+bool BondedParticle::IsBondedTo(BondedParticle * const BondPartner)
+{
+  bool status = false;
+
+  for (BondList::iterator runner = ListOfBonds.begin(); runner != ListOfBonds.end(); runner++) {
+    status = status || ((*runner)->Contains(BondPartner));
+  }
+  return status;
+};
+

src/atom_bondedparticle.hpp

@@ -39 +39 @@
   bool RegisterBond(bond *Binder);
   bool UnregisterBond(bond *Binder);
+  bool IsBondedTo(BondedParticle * const BondPartner);
   void UnregisterAllBond();
   int CountBonds() const;

src/builder.cpp

@@ -53 +53 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "boundary.hpp"
 #include "config.hpp"
@@ -840 +841 @@
           }
           if (mol->first->next != mol->last) // if connect matrix is present already, redo it
-            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance, configuration->GetIsAngstroem());
+            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
           // free memory
           delete[](Elements);
@@ -896 +897 @@
           cin >> bonddistance;
           start = clock();
-          mol->CreateAdjacencyList((ofstream *)&cout, bonddistance, configuration->GetIsAngstroem());
+          mol->CreateAdjacencyList((ofstream *)&cout, bonddistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
           end = clock();
           cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
@@ -1555 +1556 @@
                 class StackClass<bond *> *BackEdgeStack = NULL;
                 class StackClass<bond *> *LocalBackEdgeStack = NULL;
-                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr]), configuration.GetIsAngstroem());
+                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr]), configuration.GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
                 Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, BackEdgeStack);
                 if (Subgraphs != NULL) {
@@ -1912 +1913 @@
                 cout << Verbose(0) << "Creating connection matrix..." << endl;
                 start = clock();
-                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem());
+                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
                 cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
                 if (mol->first->next != mol->last) {

src/molecule.hpp

@@ -35 +35 @@
 class atom;
 class bond;
+class BondedParticle;
+class BondGraph;
 class element;
 class ForceMatrix;
@@ -238 +240 @@
   /// Initialising routines in fragmentation
   void CreateAdjacencyListFromDbondFile(ofstream *out, ifstream *output);
-  void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
+  void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
   int CorrectBondDegree(ofstream *out);
   void OutputBondsList(ofstream *out);

src/molecule_graph.cpp

@@ -8 +8 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "config.hpp"
 #include "element.hpp"
@@ -92 +93 @@
  * \param bonddistance length of linked cells (i.e. maximum minimal length checked)
  * \param IsAngstroem whether coordinate system is gauged to Angstroem or Bohr radii
- */
-void molecule::CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem)
-{
-
+ * \param *minmaxdistance function to give upper and lower bound on whether particle is bonded to some other
+ * \param *BG BondGraph with the member function above or NULL, if just standard covalent should be used.
+ */
+void molecule::CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem, void (BondGraph::*minmaxdistance)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG)
+{
   atom *Walker = NULL;
   atom *OtherWalker = NULL;
   atom **AtomMap = NULL;
   int n[NDIM];
-  double distance, MinDistance, MaxDistance;
+  double MinDistance, MaxDistance;
   LinkedCell *LC = NULL;
+  bool free_BG = false;
+
+  if (BG == NULL) {
+    BG = new BondGraph(IsAngstroem);
+    free_BG = true;
+  }
 
   BondDistance = bonddistance; // * ((IsAngstroem) ? 1. : 1./AtomicLengthToAngstroem);
@@ -146 +154 @@
                           OtherWalker = AtomMap[(*OtherRunner)->nr];
                           //*out << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
-                          MinDistance = OtherWalker->type->CovalentRadius + Walker->type->CovalentRadius;
-                          MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
-                          MaxDistance = MinDistance + BONDTHRESHOLD;
-                          MinDistance -= BONDTHRESHOLD;
-                          distance = OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size);
-                          if ((OtherWalker->father->nr > Walker->father->nr) && (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance)) { // create bond if distance is smaller
+                          (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+                          const double distance = OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size);
+                          const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
+                          if ((OtherWalker->father->nr > Walker->father->nr) && (status)) { // create bond if distance is smaller
                             //*out << Verbose(1) << "Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << "." << endl;
                             AddBond(Walker->father, OtherWalker->father, 1); // also increases molecule::BondCount
@@ -176 +182 @@
     *out << Verbose(1) << "AtomCount is " << AtomCount << ", thus no bonds, no connections!." << endl;
   *out << Verbose(0) << "End of CreateAdjacencyList." << endl;
+  if (free_BG)
+    delete(BG);
 }
 ;

src/unittests/Makefile.am

@@ -20 +20 @@
 AnalysisPairCorrelationUnitTest_LDADD = ../libmolecuilder.a
 
-BondGraphUnitTest_SOURCES = ../bondgraph.cpp ../bondgraph.hpp bondgraphunittest.cpp bondgraphunittest.hpp
+BondGraphUnitTest_SOURCES = bondgraphunittest.cpp bondgraphunittest.hpp
 BondGraphUnitTest_LDADD = ../libmolecuilder.a