Changeset 9879f6 for src/helpers.hpp

Timestamp:

Mar 5, 2010, 10:16:47 AM (16 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

d3347e

Parents:

e87acf

git-author:

Frederik Heber <heber@…> (03/05/10 10:08:44)

git-committer:

Frederik Heber <heber@…> (03/05/10 10:16:47)

Message:

Huge Refactoring due to class molecule now being an STL container.

• molecule::start and molecule::end were dropped. Hence, the usual construct Walker = start while (Walker->next != end) {

Walker = walker->next
...

}
was changed to
for (molecule::iterator iter = begin(); iter != end(); ++iter) {

...

}
and (*iter) used instead of Walker.

• Two build errors remain (beside some more in folder Actions, Patterns and unittest) in molecule_pointcloud.cpp and molecule.cpp
• lists.cpp was deleted as specialization of atom* was not needed anymore
• link, unlink, add, remove, removewithoutcheck all are not needed for atoms anymore, just for bonds (where first, last entries remain in molecule)
• CreateFatherLookupTable() was put back into class molecule.
• molecule::InternalPointer is now an iterator
• class PointCloud: GoToPrevious() and GetTerminalPoint() were dropped as not needed.
• some new STL functions in class molecule: size(), empty(), erase(), find() and insert()

File:

• src/helpers.hpp (modified) (1 diff)

src/helpers.hpp

@@ -100 +100 @@
 };
 
-/** Creates a lookup table for true father's Atom::Nr -> atom ptr.
- * \param *start begin of chain list
- * \paran *end end of chain list
- * \param **Lookuptable pointer to return allocated lookup table (should be NULL on start)
- * \param count optional predetermined size for table (otherwise we set the count to highest true father id)
- * \return true - success, false - failure
- */
-template <typename T> bool CreateFatherLookupTable(T *start, T *end, T **&LookupTable, int count = 0)
-{
-  bool status = true;
-  T *Walker = NULL;
-  int AtomNo;
-
-  if (LookupTable != NULL) {
-    Log() << Verbose(0) << "Pointer for Lookup table is not NULL! Aborting ..." <<endl;
-    return false;
-  }
-
-  // count them
-  if (count == 0) {
-    Walker = start;
-    while (Walker->next != end) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron
-      Walker = Walker->next;
-      count = (count < Walker->GetTrueFather()->nr) ? Walker->GetTrueFather()->nr : count;
-    }
-  }
-  if (count <= 0) {
-    Log() << Verbose(0) << "Count of lookup list is 0 or less." << endl;
-    return false;
-  }
-
-  // allocate and fill
-  LookupTable = Calloc<T*>(count, "CreateFatherLookupTable - **LookupTable");
-  if (LookupTable == NULL) {
-    eLog() << Verbose(0) << "LookupTable memory allocation failed!" << endl;
-    performCriticalExit();
-    status = false;
-  } else {
-    Walker = start;
-    while (Walker->next != end) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron
-      Walker = Walker->next;
-      AtomNo = Walker->GetTrueFather()->nr;
-      if ((AtomNo >= 0) && (AtomNo < count)) {
-        //*out << "Setting LookupTable[" << AtomNo << "] to " << *Walker << endl;
-        LookupTable[AtomNo] = Walker;
-      } else {
-        Log() << Verbose(0) << "Walker " << *Walker << " exceeded range of nuclear ids [0, " << count << ")." << endl;
-        status = false;
-        break;
-      }
-    }
-  }
-
-  return status;
-};
-
 /** Frees a two-dimensional array.
  * \param *ptr pointer to array