Changeset 8c001a for src/molecule.cpp

Timestamp:

Jan 10, 2015, 5:14:21 PM (11 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, 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:

739ee9

Parents:

7b38d3

git-author:

Frederik Heber <heber@…> (11/05/14 19:19:42)

git-committer:

Frederik Heber <heber@…> (01/10/15 17:14:21)

Message:

GLMoleculeObject_atoms and .._bonds are now children of .._molecule.

• GLMoleculeObject::initialize() is now virtual.
• .._molecule is now draw()ing its children, i.e. initialize() of .._molecule calls in turn those of .._atom and .._bond. Similarly with draw.
• molecule has a lastchangedatom member variable now.
• FIX: molecule::getBoundingSphere() did not check for no atoms.

File:

• src/molecule.cpp (modified) (5 diffs)

src/molecule.cpp

@@ -146 +146 @@
   OBSERVE;
   if(atomIdPool.reserveId(newNr)){
+    _lastchangedatom = target;
     NOTIFY(AtomNrChanged);
     if (oldNr != -1)  // -1 is reserved and indicates no number
@@ -207 +208 @@
 {
   OBSERVE;
-  NOTIFY(AtomRemoved);
   const_iterator iter = loc;
   ++iter;
   atom * const _atom = const_cast<atom *>(*loc);
+  {
+    _lastchangedatom = _atom;
+    NOTIFY(AtomRemoved);
+  }
   atomIds.erase( _atom->getId() );
   {
@@ -226 +230 @@
 {
   OBSERVE;
-  NOTIFY(AtomRemoved);
+  {
+    _lastchangedatom = key;
+    NOTIFY(AtomRemoved);
+  }
   const_iterator iter = find(key);
   if (iter != end()){
@@ -247 +254 @@
   OBSERVE;
   NOTIFY(AtomInserted);
+  _lastchangedatom = key;
   std::pair<iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
@@ -974 +982 @@
     for(const_iterator iter = begin(); iter != end(); ++iter)
       center += (*iter)->getPosition();
-    center *= 1./(double)size();
+    if (begin() != end())
+      center *= 1./(double)size();
     for(const_iterator iter = begin(); iter != end(); ++iter) {
       const Vector &position = (*iter)->getPosition();