Changeset 0d5dce for src/molecule.cpp

Timestamp:

Jun 24, 2010, 10:20:24 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:

8f822c

Parents:

f932b7 (diff), da3024 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'StructureRefactoring' into Shapes

File:

• src/molecule.cpp (modified) (7 diffs)

src/molecule.cpp

@@ -42 +42 @@
   NoCyclicBonds(0), BondDistance(0.),  ActiveFlag(false), IndexNr(-1),
   formula(this,boost::bind(&molecule::calcFormula,this),"formula"),
-  AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(begin())
+  AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(atoms.begin())
 {
 
@@ -146 +146 @@
   iter--;
   atom* atom = *loc;
-  atoms.erase( loc );
+  atomIds.erase( atom->getId() );
+  atoms.remove( atom );
   atom->removeFromMolecule();
   return iter;
@@ -156 +157 @@
   molecule::const_iterator iter = find(key);
   if (iter != end()){
-    atoms.erase( iter++ );
+    atomIds.erase( key->getId() );
+    atoms.remove( key );
     key->removeFromMolecule();
   }
@@ -164 +166 @@
 molecule::const_iterator molecule::find ( atom * key ) const
 {
-  return atoms.find( key );
+  molecule::const_iterator iter;
+  for (molecule::const_iterator Runner = begin(); Runner != end(); ++Runner) {
+    if (*Runner == key)
+      return molecule::const_iterator(Runner);
+  }
+  return molecule::const_iterator(atoms.end());
 }
 
 pair<molecule::iterator,bool> molecule::insert ( atom * const key )
 {
-  pair<atomSet::iterator,bool> res = atoms.insert(key);
-  return pair<iterator,bool>(iterator(res.first,this),res.second);
+  pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
+  if (res.second) { // push atom if went well
+    atoms.push_back(key);
+    return pair<iterator,bool>(molecule::iterator(--end()),res.second);
+  } else {
+    return pair<iterator,bool>(molecule::iterator(end()),res.second);
+  }
 }
 
 bool molecule::containsAtom(atom* key){
-  return atoms.count(key);
+  return (find(key) != end());
 }
 
@@ -790 +802 @@
   for (molecule::iterator iter = begin(); !empty(); iter = begin())
       erase(iter);
+  return empty();
 };
 
@@ -1010 +1023 @@
   configuration.MaxPsiDouble /= 2;
   configuration.PsiType = (configuration.PsiMaxNoDown == configuration.PsiMaxNoUp) ? 0 : 1;
-  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2)) {
+  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2) && ((configuration.PsiMaxNoDown != 1) || (configuration.PsiMaxNoUp != 0))) {
     configuration.ProcPEGamma /= 2;
     configuration.ProcPEPsi *= 2;
@@ -1017 +1030 @@
     configuration.ProcPEPsi = 1;
   }
-  configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.MaxPsiDouble;
+  cout << configuration.PsiMaxNoDown << ">" << configuration.PsiMaxNoUp << endl;
+  if (configuration.PsiMaxNoDown > configuration.PsiMaxNoUp) {
+    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoDown;
+    cout << configuration.PsiMaxNoDown << " " << configuration.InitMaxMinStopStep << endl;
+  } else {
+    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoUp;
+    cout << configuration.PsiMaxNoUp << " " << configuration.InitMaxMinStopStep << endl;
+  }
 };