Changeset 7fd416 for src

Timestamp:

Jun 2, 2010, 12:22:47 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, 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:

accebe

Parents:

6ef0a4

Message:

FIX: CorrelationToSurface() was broken.

• DOCU: CorrelationToSurface() is more verbose on empty molecules, molecule::doCountAtoms() is verbose on naming atoms only for high verbosity levels
• MEMFIX: ParseCommandLineOptions() - case 'CP' did not set counter to zero for re-setting active flag.
• BUGFIX: molecule::DeterminePeriodicCenter() - InverseMatrix() was called with cell_size instead of full matrix.
• rewritten MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() a bit:
  • molname and contained atoms are given
  • no more stupid map, atoms are directly transfered from Leaf to molecules[]
  • mol that contained all was not destroyed after use

Location:

src

Files:

• analysis_correlation.cpp (modified) (2 diffs)
• builder.cpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule_geometry.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (5 diffs)

src/analysis_correlation.cpp

@@ -262 +262 @@
     if ((*MolWalker)->ActiveFlag) {
       DoLog(1) && (Log() << Verbose(1) << "Current molecule is " << (*MolWalker)->name << "." << endl);
-      for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
-        //Log() << Verbose(3) << "Current atom is " << *(*iter) << "." << endl;
+      if ((*MolWalker)->empty())
+        DoLog(1) && (1) && (Log() << Verbose(1) << "\t is empty." << endl);
+      for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
+        DoLog(1) && (Log() << Verbose(1) << "\tCurrent atom is " << *(*iter) << "." << endl);
         if ((type == NULL) || ((*iter)->type == type)) {
           TriangleIntersectionList Intersections((*iter)->node,Surface,LC);
@@ -271 +273 @@
         }
       }
-    } else
+    } else {
       DoLog(1) && (Log() << Verbose(1) << "molecule " << (*MolWalker)->name << " is not active." << endl);
+    }
 
   return outmap;

src/builder.cpp

@@ -1911 +1911 @@
                           output.close();
                           binoutput.close();
+                          counter = 0;
                           for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++)
                             (*BigFinder)->ActiveFlag = Actives[counter++];

src/molecule.cpp

@@ -963 +963 @@
     sstr << (*iter)->type->symbol << (*iter)->nr+1;
     (*iter)->setName(sstr.str());
-    Log() << Verbose(3) << "Naming atom nr. " << (*iter)->nr << " " << (*iter)->getName() << "." << endl;
+    DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << (*iter)->nr << " " << (*iter)->getName() << "." << endl);
     i++;
   }

src/molecule_geometry.cpp

@@ -266 +266 @@
   double * const cell_size = World::getInstance().getDomain();
   double *matrix = ReturnFullMatrixforSymmetric(cell_size);
-  double *inversematrix = InverseMatrix(cell_size);
+  double *inversematrix = InverseMatrix(matrix);
   double tmp;
   bool flag;

src/moleculelist.cpp

@@ -754 +754 @@
     World::getInstance().destroyMolecule(*MolRunner);
   }
-  // 0b. remove all bonds
+  // 0b. remove all bonds and construct a molecule with all atoms
   molecule *mol = World::getInstance().createMolecule();
   vector <atom *> allatoms = World::getInstance().getAllAtoms();
@@ -789 +789 @@
   char number[MAXSTRINGSIZE];
   molecule **molecules = new molecule *[MolCount];
+  MoleculeLeafClass *MolecularWalker = Subgraphs;
   for (int i=0;i<MolCount;i++) {
+    MolecularWalker = MolecularWalker->next;
     molecules[i] = World::getInstance().createMolecule();
     molecules[i]->ActiveFlag = true;
@@ -798 +800 @@
     }
     DoLog(1) && (Log() << Verbose(1) << "MolName is " << molecules[i]->name << endl);
+    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); iter != MolecularWalker->Leaf->end(); ++iter) {
+      DoLog(1) && (Log() << Verbose(1) << **iter << endl);
+    }
     insert(molecules[i]);
   }
@@ -803 +808 @@
   // 4b. create and fill map of which atom is associated to which connected molecule (note, counting starts at 1)
   int FragmentCounter = 0;
-  int *MolMap = new int[mol->getAtomCount()];
-  for (int i=0;i<mol->getAtomCount();i++)
-    MolMap[i] = 0;
-  MoleculeLeafClass *MolecularWalker = Subgraphs;
+  map<int, atom *> AtomToFragmentMap;
+  MolecularWalker = Subgraphs;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
-    for (molecule::const_iterator iter = MolecularWalker->Leaf->begin(); iter != MolecularWalker->Leaf->end(); ++iter) {
-      MolMap[(*iter)->GetTrueFather()->nr] = FragmentCounter+1;
+    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); !MolecularWalker->Leaf->empty(); iter = MolecularWalker->Leaf->begin()) {
+      atom * Walker = *iter;
+      DoLog(1) && (Log() << Verbose(1) << "Re-linking " << Walker << "..." << endl);
+      MolecularWalker->Leaf->erase(iter);
+      molecules[FragmentCounter]->AddAtom(Walker);    // counting starts at 1
     }
     FragmentCounter++;
   }
-
-  // 4c. relocate atoms to new molecules and remove from Leafs
-  for (molecule::iterator iter = mol->begin(); !mol->empty(); iter = mol->begin()) {
-    const int count = mol->getAtomCount();
-    if (((*iter)->nr <0) || ((*iter)->nr >= count)) {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Index " << (*iter)->nr << " of atom " << **iter << " in molecule of " << count << " atoms is invalid!" << endl);
-      performCriticalExit();
-    }
-    const int Index = MolMap[(*iter)->nr];
-    if (Index != 0) {
-      DoLog(3) && (Log() << Verbose(3) << "Re-linking " << **iter << "..." << endl);
-      molecules[Index-1]->AddAtom((*iter));    // counting starts at 1
-      mol->erase(iter);
-    } else {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Atom " << **iter << " not associated to molecule!" << endl);
-      performCriticalExit();
-    }
-  }
+  World::getInstance().destroyMolecule(mol);
+
   // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
   // TODO: check whether this is really not needed anymore
@@ -841 +831 @@
   }
   delete(MolecularWalker);
-  delete[](MolMap);
   delete[](molecules);
   DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);