Changeset 357fba for src/molecules.cpp

Timestamp:

Aug 3, 2009, 2:48:42 PM (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, 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:

a80fbdf, caf4ba

Parents:

2319ed

Message:

Huge refactoring of Tesselation routines, but not finished yet.

• new file tesselation.cpp with all of classes tesselation, Boundary..Set and CandidatesForTesselationOB
• new file tesselationhelper.cpp with all auxiliary functions.
• boundary.cpp just contains super functions, combininb molecule and Tesselation pointers
• new pointer molecule::TesselStruct
• PointMap, LineMap, TriangleMap DistanceMap have been moved from molecules.hpp to tesselation.hpp
• new abstract class PointCloud and TesselPoint
• atom inherits TesselPoint
• molecule inherits PointCloud (i.e. a set of TesselPoints) and implements all virtual functions for the chained list
• TriangleFilesWritten is thrown out, intermediate steps are written in find_nonconvex_border and not in find_next_triangle()
• LinkedCell class uses TesselPoint as its nodes, i.e. as long as any class inherits TesselPoint, it may make use of LinkedCell as well and a PointCloud is used to initialize
• class atom and bond definitions have been moved to own header files

NOTE: This is not bugfree yet. Tesselation of heptan produces way too many triangles, but runs without faults or leaks.

File:

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

src/molecules.cpp

@@ -42 +42 @@
   end->father = NULL;
   link(start,end);
+  InternalPointer = start;
   // init bond chain list
   first = new bond(start, end, 1, -1);
@@ -82 +83 @@
   delete(end);
   delete(start);
+};
+
+
+/** Determine center of all atoms.
+ * \param *out output stream for debugging
+ * \return pointer to allocated with central coordinates
+ */
+Vector *molecule::GetCenter(ofstream *out)
+{
+  Vector *center = DetermineCenterOfAll(out);
+  return center;
+};
+
+/** Return current atom in the list.
+ * \return pointer to atom or NULL if none present
+ */
+TesselPoint *molecule::GetPoint()
+{
+  if ((InternalPointer != start) && (InternalPointer != end))
+    return InternalPointer;
+  else
+    return NULL;
+};
+
+/** Return pointer to one after last atom in the list.
+ * \return pointer to end marker
+ */
+TesselPoint *molecule::GetTerminalPoint()
+{
+  return end;
+};
+
+/** Go to next atom.
+ * Stops at last one.
+ */
+void molecule::GoToNext()
+{
+  if (InternalPointer->next != end)
+    InternalPointer = InternalPointer->next;
+};
+
+/** Go to previous atom.
+ * Stops at first one.
+ */
+void molecule::GoToPrevious()
+{
+  if (InternalPointer->previous != start)
+    InternalPointer = InternalPointer->previous;
+};
+
+/** Goes to first atom.
+ */
+void molecule::GoToFirst()
+{
+  InternalPointer = start->next;
+};
+
+/** Goes to last atom.
+ */
+void molecule::GoToLast()
+{
+  InternalPointer = end->previous;
+};
+
+/** Checks whether we have any atoms in molecule.
+ * \return true - no atoms, false - not empty
+ */
+bool molecule::IsEmpty()
+{
+  return (start->next == end);
+};
+
+/** Checks whether we are at the last atom
+ * \return true - current atom is last one, false - is not last one
+ */
+bool molecule::IsLast()
+{
+  return (InternalPointer->next == end);
 };