Changeset 1024cb for src/molecule_pointcloud.cpp

Timestamp:

May 31, 2010, 5:32:27 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:

e08c46

Parents:

42af9e (diff), a7b761b (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.

git-author:

Frederik Heber <heber@…> (05/31/10 17:29:30)

git-committer:

Frederik Heber <heber@…> (05/31/10 17:32:27)

Message:

Merge commit 'jupiter/MoleculeStartEndSwitch' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp
molecuilder/src/unittests/listofbondsunittest.cpp

Integration of MoleculeStartEndSwitch had the following consequences:

• no more AtomCount -> getAtomCount()
• no more start/end -> begin(), end() and iterator
• no more decent ordering in atomic ids (hence, Simple_configuration/8 and Domain/5, Domain/6 now check by comparing sorted xyz, not confs)

There is still a huge problem with bonds. One test runs into an endless loop.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule_pointcloud.cpp (modified) (2 diffs)

src/molecule_pointcloud.cpp

@@ -8 +8 @@
 #include "atom.hpp"
 #include "config.hpp"
+#include "info.hpp"
 #include "memoryallocator.hpp"
 #include "molecule.hpp"
@@ -31 +32 @@
 };
 
-/** Return current atom in the list.
- * \return pointer to atom or NULL if none present
+
+/** PointCloud implementation of GoPoint
+ * Uses atoms and STL stuff.
  */
-TesselPoint *molecule::GetPoint() const
+TesselPoint* molecule::GetPoint() const
 {
-  if ((InternalPointer != start) && (InternalPointer != end))
-    return InternalPointer;
-  else
-    return NULL;
+  Info FunctionInfo(__func__);
+  return (*InternalPointer);
 };
 
-/** Return pointer to one after last atom in the list.
- * \return pointer to end marker
- */
-TesselPoint *molecule::GetTerminalPoint() const
-{
-  return end;
-};
-
-/** Return the greatest index of all atoms in the list.
- * \return greatest index
- */
-int molecule::GetMaxId() const
-{
-  return last_atom;
-};
-
-/** Go to next atom.
- * Stops at last one.
+/** PointCloud implementation of GoToNext.
+ * Uses atoms and STL stuff.
  */
 void molecule::GoToNext() const
 {
-  if (InternalPointer != end)
-    InternalPointer = InternalPointer->next;
+  Info FunctionInfo(__func__);
+  if (InternalPointer != atoms.end())
+    InternalPointer++;
 };
 
-/** Go to previous atom.
- * Stops at first one.
- */
-void molecule::GoToPrevious() const
-{
-  if (InternalPointer->previous != start)
-    InternalPointer = InternalPointer->previous;
-};
-
-/** Goes to first atom.
+/** PointCloud implementation of GoToFirst.
+ * Uses atoms and STL stuff.
  */
 void molecule::GoToFirst() const
 {
-  InternalPointer = start->next;
+  Info FunctionInfo(__func__);
+  InternalPointer = atoms.begin();
 };
 
-/** Goes to last atom.
- */
-void molecule::GoToLast() const
-{
-  InternalPointer = end->previous;
-};
-
-/** Checks whether we have any atoms in molecule.
- * \return true - no atoms, false - not empty
+/** PointCloud implementation of IsEmpty.
+ * Uses atoms and STL stuff.
  */
 bool molecule::IsEmpty() const
 {
-  return (start->next == end);
+  Info FunctionInfo(__func__);
+  return (empty());
 };
 
-/** Checks whether we are at the last atom
- * \return true - current atom is last one, false - is not last one
+/** PointCloud implementation of IsLast.
+ * Uses atoms and STL stuff.
  */
 bool molecule::IsEnd() const
 {
-  return (InternalPointer == end);
+  Info FunctionInfo(__func__);
+  return (InternalPointer == atoms.end());
 };
+
+int molecule::GetMaxId() const {
+  return getAtomCount();
+}