Changeset efe516

Timestamp:

Mar 2, 2011, 9:53:09 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:

7d8aa0

Parents:

2fa1dc

git-author:

Frederik Heber <heber@…> (03/01/11 14:16:44)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:09)

Message:

Removed bond::nr.

• has only been used by BreadthFirstSearchAdd.
• changed BreadthFirstSearchAdd::AddedBonds into map<bond*,bond*>.

Location:

src

Files:

• Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) (1 diff)
• Bond/bond.cpp (modified) (2 diffs)
• Bond/bond.hpp (modified) (2 diffs)
• Graph/BondGraph.hpp (modified) (1 diff)
• Graph/BreadthFirstSearchAdd.cpp (modified) (3 diffs)
• Graph/BreadthFirstSearchAdd.hpp (modified) (1 diff)
• atom_bondedparticle.cpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (5 diffs)

src/Actions/FragmentationAction/CreateAdjacencyAction.cpp

@@ -141 +141 @@
                             if (status) { // create bond if distance is smaller
 //                              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++);
+                              bond * const Binder = new bond(Walker->father, OtherWalker->father, 1);
+                              BondCount++;
                               Walker->father->RegisterBond(WorldTime::getTime(),Binder);
                               OtherWalker->father->RegisterBond(WorldTime::getTime(),Binder);

src/Bond/bond.cpp

@@ -34 +34 @@
   rightatom(NULL),
   HydrogenBond(0),
-  BondDegree(0),
-  nr(-1)
+  BondDegree(0)
 {};
 
@@ -44 +43 @@
  * \param number increasing index
  */
-bond::bond(atom *left, atom *right, const int degree, const int number) :
+bond::bond(atom *left, atom *right, const int degree) :
   leftatom(left),
   rightatom(right),
   HydrogenBond(0),
-  BondDegree(degree),
-  nr(number)
+  BondDegree(degree)
 {
   if ((left != NULL) && (right != NULL)) {

src/Bond/bond.hpp

@@ -41 +41 @@
   int HydrogenBond;  //!< Number of hydrogen atoms in the bond
   int BondDegree;    //!< single, double, triple, ... bond
-  int nr;           //!< unique number in a molecule, updated by BondGraph::CreateAdjacencyForList()
 
   atom * GetOtherAtom(const ParticleInfo * const Atom) const;
@@ -51 +50 @@
 
   bond();
-  bond(atom *left, atom *right, const int degree=1, const int number=0);
+  bond(atom *left, atom *right, const int degree=1);
   ~bond();
-
 };
 

src/Graph/BondGraph.hpp

@@ -230 +230 @@
 
       LOG(3, "INFO: Creating bond between atoms " << atom1 << " and " << atom2 << ".");
-      bond * const Binder = new bond(Walker, OtherWalker, 1, -1);
+      bond * const Binder = new bond(Walker, OtherWalker, 1);
       Walker->RegisterBond(WorldTime::getTime(), Binder);
       OtherWalker->RegisterBond(WorldTime::getTime(), Binder);

src/Graph/BreadthFirstSearchAdd.cpp

@@ -75 +75 @@
       AddedAtomList[OtherAtom->getNr()] = Mol->AddCopyAtom(OtherAtom);
       DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->getName());
-      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
-      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder->nr]) << ", ");
+      AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder]) << ", ");
     } else { // this code should actually never come into play (all GraphEdge::white atoms are not yet present in BondMolecule, that's why they are GraphEdge::white in the first place)
       DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
-      if (AddedBondList[Binder->nr] == NULL) {
-        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
-        DoLog(0) && (Log() << Verbose(0) << ", added Bond " << *(AddedBondList[Binder->nr]));
+      if (AddedBondList[Binder] == NULL) {
+        AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+        DoLog(0) && (Log() << Verbose(0) << ", added Bond " << *(AddedBondList[Binder]));
       } else
         DoLog(0) && (Log() << Verbose(0) << ", not added Bond ");
@@ -96 +96 @@
     if (!Binder->Cyclic)
       DoLog(0) && (Log() << Verbose(0) << ", is not part of a cyclic bond, saturating bond with Hydrogen." << endl);
-    if (AddedBondList[Binder->nr] == NULL) {
+    if (AddedBondList[Binder] == NULL) {
       if ((AddedAtomList[OtherAtom->getNr()] != NULL)) { // .. whether we add or saturate
-        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+        AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
       } else {
 #ifdef ADDHYDROGEN
@@ -114 +114 @@
   DoLog(3) && (Log() << Verbose(3) << "Not Adding, has already been visited." << endl);
   // This has to be a cyclic bond, check whether it's present ...
-  if (AddedBondList[Binder->nr] == NULL) {
+  if (AddedBondList[Binder] == NULL) {
     if ((Binder != Bond) && (Binder->Cyclic) && (((ShortestPathList[Walker->getNr()] + 1) < BondOrder))) {
-      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+      AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
     } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
 #ifdef ADDHYDROGEN

src/Graph/BreadthFirstSearchAdd.hpp

@@ -69 +69 @@
   int ComponentNr;
   std::map<atomId_t, atom *> AddedAtomList;
-  std::map<int, bond *> AddedBondList;
+  std::map<bond *, bond *> AddedBondList; //!< maps from father bond to son
 
   bool IsAngstroem;

src/atom_bondedparticle.cpp

@@ -104 +104 @@
   }
 
-  bond* newBond = new bond((atom*) this, (atom*) Partner, 1, 0);
+  bond* newBond = new bond((atom*) this, (atom*) Partner, 1);
   RegisterBond(_step, newBond);
   Partner->RegisterBond(_step, newBond);

src/molecule.cpp

@@ -744 +744 @@
   ASSERT(FindAtom(atom2->getNr()),"Second atom in bond-creation was not part of molecule");
 
-  Binder = new bond(atom1, atom2, degree, getBondCount());
+  Binder = new bond(atom1, atom2, degree);
   atom1->RegisterBond(WorldTime::getTime(), Binder);
   atom2->RegisterBond(WorldTime::getTime(), Binder);

src/moleculelist.cpp

@@ -512 +512 @@
       strcpy(PathBackup, path);
     else {
-      DoeLog(0) && (eLog()<< Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl);
+      ELOG(0, "OutputConfigForListOfFragments: NULL default path obtained from config!");
       performCriticalExit();
     }
@@ -521 +521 @@
     }
 
-    // output xyz file
-    FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
-    FragmentName = prefix + FragmentNumber + ".conf.xyz";
-    outputFragment.open(FragmentName.c_str(), ios::out);
-    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
-    if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
-      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
-    else
-      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
-    result = result && intermediateResult;
-    outputFragment.close();
-    outputFragment.clear();
-
-    // list atoms in fragment for debugging
-    DoLog(2) && (Log() << Verbose(2) << "Contained atoms: ");
-    for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
-      DoLog(0) && (Log() << Verbose(0) << (*iter)->getName() << " ");
-    }
-    DoLog(0) && (Log() << Verbose(0) << endl);
+    {
+      // list atoms in fragment for debugging
+      std::stringstream output;
+      output << "Contained atoms: ";
+      for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
+        output << (*iter)->getName() << " ";
+      }
+      LOG(2, output.str());
+    }
+
+    {
+      // output xyz file
+      FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
+      FragmentName = prefix + FragmentNumber + ".conf.xyz";
+      outputFragment.open(FragmentName.c_str(), ios::out);
+      std::stringstream output;
+      output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ... ";
+      if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
+        output << " done.";
+      else
+        output << " failed.";
+      LOG(3, output.str());
+      result = result && intermediateResult;
+      outputFragment.close();
+      outputFragment.clear();
+    }
 
     // center on edge
@@ -554 +561 @@
     (*ListRunner)->Translate(&BoxDimension);
 
-    // also calculate necessary orbitals
-    //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
-
     // change path in config
     FragmentName = PathBackup;
@@ -565 +569 @@
     World::getInstance().getConfig()->SetDefaultPath(FragmentName.c_str());
 
-    // and save as config
-    FragmentName = prefix + FragmentNumber + ".conf";
-    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
-    if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
-      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
-    else
-      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
-    result = result && intermediateResult;
+    {
+      // and save as config
+      FragmentName = prefix + FragmentNumber + ".conf";
+      std::stringstream output;
+      output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ... ";
+      if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
+        output << " done.";
+      else
+        output << " failed.";
+      LOG(3, output.str());
+      result = result && intermediateResult;
+    }
 
     // restore old config
     World::getInstance().getConfig()->SetDefaultPath(PathBackup);
 
-    // and save as mpqc input file
-    FragmentName = prefix + FragmentNumber + ".conf";
-    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
-    if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
-      DoLog(2) && (Log() << Verbose(2) << " done." << endl);
-    else
-      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
+    {
+      // and save as mpqc input file
+      stringstream output;
+      FragmentName = prefix + FragmentNumber + ".conf";
+      output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ... ";
+      if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
+        output << " done.";
+      else
+        output << " failed.";
+      LOG(3, output.str());
+    }
 
     result = result && intermediateResult;
@@ -590 +602 @@
     delete[](FragmentNumber);
   }
-  DoLog(0) && (Log() << Verbose(0) << " done." << endl);
+  LOG(0, "STATUS: done.");
 
   // printing final number
-  DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
+  LOG(2, "INFO: Final number of fragments: " << FragmentCounter << ".");
 
   // printing final number
-  DoLog(0) && (Log() << Verbose(0) << "For " << count << " fragments periodic correction would have been necessary." << endl);
+  LOG(2, "INFO: For " << count << " fragments periodic correction would have been necessary.");
 
   // restore cell_size