Changeset 357fba for src/atom.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, 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:

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/atom.cpp (modified) (5 diffs)

src/atom.cpp

@@ -5 +5 @@
  */
 
-#include "molecules.hpp"
+#include "atom.hpp"
 
 /************************************* Functions for class atom *************************************/
@@ -13 +13 @@
 atom::atom()
 {
-  Name = NULL;
+  father = this;  // generally, father is itself
   previous = NULL;
   next = NULL;
-  father = this;  // generally, father is itself
   Ancestor = NULL;
   type = NULL;
   sort = NULL;
   FixedIon = 0;
-  nr = -1;
   GraphNr = -1;
   ComponentNr = NULL;
@@ -29 +27 @@
   AdaptiveOrder = 0;
   MaxOrder = false;
+  // set LCNode::Vector to our Vector
+  node = &x;
 };
 
 /** Constructor of class atom.
- *
  */
 atom::atom(atom *pointer)
@@ -41 +40 @@
   father = this;  // generally, father is itself
   Ancestor = NULL;
+  GraphNr = -1;
+  ComponentNr = NULL;
+  IsCyclic = false;
+  SeparationVertex = false;
+  LowpointNr = -1;
+  AdaptiveOrder = 0;
+  MaxOrder = false;
   type = pointer->type;  // copy element of atom
   x.CopyVector(&pointer->x); // copy coordination
@@ -54 +60 @@
 atom::~atom()
 {
-  Free((void **)&Name, "atom::~atom: *Name");
   Free((void **)&ComponentNr, "atom::~atom: *ComponentNr");
 };