Changeset 073a9e4

Timestamp:

Feb 24, 2011, 7:26:14 PM (14 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:

1e6249

Parents:

d557374

git-author:

Frederik Heber <heber@…> (02/24/11 14:32:36)

git-committer:

Frederik Heber <heber@…> (02/24/11 19:26:14)

Message:

BondedParticle::(Un)RegisterBond,AddBond,IsBondedTo with step.

• adding, removing and checking of bonds at a desired time step.

Location:

src

Files:

• Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) (1 diff)
• Parser/PdbParser.cpp (modified) (3 diffs)
• Parser/TremoloParser.cpp (modified) (1 diff)
• Parser/unittests/ParserTremoloUnitTest.cpp (modified) (3 diffs)
• atom_bondedparticle.cpp (modified) (3 diffs)
• atom_bondedparticle.hpp (modified) (1 diff)
• molecule.cpp (modified) (2 diffs)
• unittests/BondGraphUnitTest.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/ConstructBondGraphAction.cpp

@@ -140 +140 @@
 //                              Log() << Verbose(1) << "Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << "." << endl;
                               bond * const Binder = new bond(Walker->father, OtherWalker->father, 1, BondCount++);
-                              Walker->father->RegisterBond(Binder);
-                              OtherWalker->father->RegisterBond(Binder);
+                              Walker->father->RegisterBond(WorldTime::getTime(),Binder);
+                              OtherWalker->father->RegisterBond(WorldTime::getTime(),Binder);
                             } else {
 //                              Log() << Verbose(1) << "Not Adding: distance too great." << endl;

src/Parser/PdbParser.cpp

@@ -24 +24 @@
 #include "CodePatterns/toString.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -32 +31 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Parser/PdbParser.hpp"
+#include "World.hpp"
+#include "WorldTime.hpp"
 
 #include <map>
@@ -522 +523 @@
 //    DoLog(1) && (Log() << Verbose(1) << "Adding Bond (" << getAtomId(id) << "," << getAtomId(*iter) << ")" << std::endl);
     atom * const _Otheratom = World::getInstance().getAtom(AtomById(getSerial(*iter)));
-    _atom->addBond(_Otheratom);
+    _atom->addBond(WorldTime::getTime(), _Otheratom);
   }
 }

src/Parser/TremoloParser.cpp

@@ -458 +458 @@
 //            << atomIdMap[*neighbor] << "|" << *neighbor << ")" << std::endl);
         World::getInstance().getAtom(AtomById(currentInfo->first))
-            ->addBond(World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
+            ->addBond(WorldTime::getTime(), World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
       }
       currentInfo->second.neighbors_processed = true;

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -24 +24 @@
 #include <cppunit/ui/text/TestRunner.h>
 
+#include "atom.hpp"
+#include "Descriptors/AtomTypeDescriptor.hpp"
+#include "element.hpp"
 #include "Parser/MpqcParser.hpp"
 #include "Parser/PdbParser.hpp"
@@ -29 +32 @@
 #include "Parser/TremoloParser.hpp"
 #include "Parser/XyzParser.hpp"
+#include "periodentafel.hpp"
 #include "World.hpp"
-#include "atom.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
-#include "Descriptors/AtomTypeDescriptor.hpp"
+#include "WorldTime.hpp"
 
 #ifdef HAVE_TESTRUNNER
@@ -165 +166 @@
   CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
   CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(8))->
-      IsBondedTo(World::getInstance().getAtom(AtomByType(1))));
+      IsBondedTo(WorldTime::getTime(), World::getInstance().getAtom(AtomByType(1))));
   input.clear();
 }

src/atom_bondedparticle.cpp

@@ -103 +103 @@
  * bond already exists.
  *
+ * @param _step time step to access
  * \param bonding partner
  */
-void BondedParticle::addBond(BondedParticle* Partner) {
-  if (IsBondedTo(Partner)) {
+void BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner) {
+  if (IsBondedTo(_step, Partner)) {
     return;
   }
 
   bond* newBond = new bond((atom*) this, (atom*) Partner, 1, 0);
-  RegisterBond(newBond);
-  Partner->RegisterBond(newBond);
+  RegisterBond(_step, newBond);
+  Partner->RegisterBond(_step, newBond);
 }
 
 /** Puts a given bond into atom::ListOfBonds.
+ * @param _step time step to access
  * \param *Binder bond to insert
  */
-bool BondedParticle::RegisterBond(bond *Binder)
+bool BondedParticle::RegisterBond(const unsigned int _step, bond *Binder)
 {
   bool status = false;
@@ -124 +126 @@
     if (Binder->Contains(this)) {
       //LOG(3,"INFO: Registering bond "<< *Binder << " with atom " << *this << " at step " << _step);
-      BondList& ListOfBonds = getListOfBonds();
+      BondList& ListOfBonds = getListOfBondsAtStep(_step);
       ListOfBonds.push_back(Binder);
       status = true;
@@ -245 +247 @@
 
 /** Checks whether there is a bond between \a this atom and the given \a *BondPartner.
+ * @param _step time step to access
  * \param *BondPartner atom to check for
  * \return true - bond exists, false - bond does not exist
  */
-bool BondedParticle::IsBondedTo(BondedParticle * const BondPartner)
+bool BondedParticle::IsBondedTo(const unsigned int _step, BondedParticle * const BondPartner) const
 {
   bool status = false;
 
-  const BondList& ListOfBonds = getListOfBonds();
-  for (BondList::const_iterator runner = ListOfBonds.begin(); runner != ListOfBonds.end(); runner++) {
+  const BondList& ListOfBonds = getListOfBondsAtStep(_step);
+  for (BondList::const_iterator runner = ListOfBonds.begin();
+      runner != ListOfBonds.end();
+      runner++) {
     status = status || ((*runner)->Contains(BondPartner));
   }

src/atom_bondedparticle.hpp

@@ -37 +37 @@
   virtual ~BondedParticle();
 
-  void addBond(BondedParticle* Partner);
-  bool RegisterBond(bond *Binder);
+  void addBond(const unsigned int _step, BondedParticle* Partner);
+  bool RegisterBond(const unsigned int _step, bond *Binder);
   bool UnregisterBond(bond *Binder);
-  bool IsBondedTo(BondedParticle * const BondPartner);
+  bool IsBondedTo(const unsigned int _step, BondedParticle * const BondPartner) const;
   void UnregisterAllBond(const unsigned int _step);
   int CountBonds() const;

src/molecule.cpp

@@ -728 +728 @@
 
   Binder = new bond(atom1, atom2, degree, BondCount++);
-  atom1->RegisterBond(Binder);
-  atom2->RegisterBond(Binder);
+  atom1->RegisterBond(WorldTime::getTime(), Binder);
+  atom2->RegisterBond(WorldTime::getTime(), Binder);
   if ((atom1->getType() != NULL) && (atom1->getType()->getAtomicNumber() != 1) && (atom2->getType() != NULL) && (atom2->getType()->getAtomicNumber() != 1))
     NoNonBonds++;
@@ -737 +737 @@
 
 /** Remove bond from bond chain list and from the both atom::ListOfBonds.
- * \todo Function not implemented yet
+ * Bond::~Bond takes care of bond removal
  * \param *pointer bond pointer
  * \return true - bound found and removed, false - bond not found/removed

src/unittests/BondGraphUnitTest.cpp

@@ -30 +30 @@
 #include "CodePatterns/Assert.hpp"
 
-#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -39 +38 @@
 #include "periodentafel.hpp"
 #include "World.hpp"
+#include "WorldTime.hpp"
 
 #include "BondGraphUnitTest.hpp"
@@ -148 +148 @@
   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(test) );
   CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule) );
-  CPPUNIT_ASSERT_EQUAL( true , (*Walker)->IsBondedTo((*Runner)) );
+  CPPUNIT_ASSERT_EQUAL( true , (*Walker)->IsBondedTo(WorldTime::getTime(), (*Runner)) );
 };