Changeset d3347e

Timestamp:

Mar 5, 2010, 11:40:30 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

75ac0c

Parents:

9879f6

git-author:

Tillmann Crueger <crueger@…> (03/05/10 11:40:05)

git-committer:

Tillmann Crueger <crueger@…> (03/05/10 11:40:30)

Message:

FIX: repaired compiler problems for latest refactoring

Location:

src

Files:

• lists.hpp (modified) (1 diff)
• memoryallocator.hpp (modified) (2 diffs)
• molecule.cpp (modified) (4 diffs)
• molecule.hpp (modified) (4 diffs)
• molecule_graph.cpp (modified) (2 diffs)
• molecule_pointcloud.cpp (modified) (3 diffs)

src/lists.hpp

@@ -8 +8 @@
 #ifndef LISTS_HPP_
 #define LISTS_HPP_
+
+class atom;
 
 /******************************** Some templates for list management ***********************************/

src/memoryallocator.hpp

@@ -115 +115 @@
 template <typename X> void Free(X** buffer, const char *msg = NULL)
 {
+  std::cout << "!!!!!!!!!!!!!!!!!removing pointer to buffer !!!!!!!!!!!!" << std::endl;
   if ((buffer == NULL) || (*buffer == NULL))
     return;
@@ -130 +131 @@
 template <typename X> void Free(X* const buffer, const char *msg = NULL)
 {
+  std::cout << "!!!!!!!!!!!!!!!!!removing direct buffer !!!!!!!!!!!!" << std::endl;
   if ((buffer == NULL))
     return;

src/molecule.cpp

@@ -31 +31 @@
  * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
  */
-molecule::molecule(const periodentafel * const teil) : elemente(teil)
+molecule::molecule(const periodentafel * const teil) : elemente(teil),
   first(new bond(0, 0, 1, -1)), last(new bond(0, 0, 1, -1)), MDSteps(0), AtomCount(0),
   BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
@@ -166 +166 @@
 pair<molecule::iterator,bool> molecule::insert ( atom * const key )
 {
-  return atoms.insert(key);
+  pair<atomSet::iterator,bool> res = atoms.insert(key);
+  return pair<iterator,bool>(iterator(res.first,this),res.second);
 }
 
@@ -937 +938 @@
 void molecule::CountAtoms()
 {
+  cout << "!!!!!!!!!!! Assigning Numbers to atoms " << endl;
   int i = size();
   if ((AtomCount == 0) || (i != AtomCount)) {
+    cout << "!!!!!!!!! Counting needed" << endl;
     Log() << Verbose(3) << "Mismatch in AtomCount " << AtomCount << " and recounted number " << i << ", renaming all." << endl;
     AtomCount = i;
@@ -958 +961 @@
     } else
       Log() << Verbose(3) << "AtomCount is still " << AtomCount << ", thus counting nothing." << endl;
+  }
+  else {
+    cout << "!!!!!!!!! Nothing changed while counting" << endl;
   }
 };

src/molecule.hpp

@@ -94 +94 @@
     typedef ObservedIterator<atomSet> iterator;
     typedef atomSet::const_iterator const_iterator;
+
     double cell_size[6];//!< cell size
     const periodentafel * const elemente; //!< periodic table with each element
@@ -120 +121 @@
     atomSet atoms; //<!set of atoms
   protected:
+    /**
+     * this iterator type should be used for internal variables, \
+     * since it will not lock
+     */
+    typedef atomSet::iterator internal_iterator;
+
+
     molecule(const periodentafel * const teil);
     virtual ~molecule();
@@ -149 +157 @@
   Vector *GetCenter() const ;
   TesselPoint *GetPoint() const ;
-  int GetMaxId() const;
+  //int GetMaxId() const;
   void GoToNext() const ;
   void GoToFirst() const ;
@@ -342 +350 @@
   private:
   int last_atom;      //!< number given to last atom
-  mutable iterator InternalPointer;  //!< internal pointer for PointCloud
+  mutable internal_iterator InternalPointer;  //!< internal pointer for PointCloud
 };
 

src/molecule_graph.cpp

@@ -136 +136 @@
     AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
     for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+      std::cout << "!!!!!!!!!!!!Copying pointer to Atom number: " << (*iter)->nr << std::endl;
       AtomMap[(*iter)->nr] = (*iter);
     }
@@ -177 +178 @@
           }
         }
+    std::cout << "trying to remove Pointer to buffer " << std::endl;
     Free(&AtomMap);
     delete (LC);

src/molecule_pointcloud.cpp

@@ -48 +48 @@
 {
   Info FunctionInfo(__func__);
-  if (InternalPointer != end())
+  if (InternalPointer != atoms.end())
     InternalPointer++;
 };
@@ -58 +58 @@
 {
   Info FunctionInfo(__func__);
-  InternalPointer = begin();
+  InternalPointer = atoms.begin();
 };
 
@@ -76 +76 @@
 {
   Info FunctionInfo(__func__);
-  return (InternalPointer == end());
+  return (InternalPointer == atoms.end());
 };