Changeset 2319ed for src/molecules.cpp

Timestamp:

Aug 3, 2009, 8:10:09 AM (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:

0dbddc, 357fba

Parents:

e1589e

Message:

We are one step further in fixing the convex hull: There are two functions of Saskia Metzler missing, but then we may proceed with testing whether the simple correction scheme of the convex envelope works, but one thing: Right now we cannot associate a Tesselation to its molecule as the snake bites it's one tail. Hence, the next commit will consist of fixing this bad-OOP issue.

• Makefile.am: Just some alphabetical resorting.
• atom::atom() new copy constructor
• builder.cpp: some output for cluster volume, molecule::AddCopyAtom() uses new copy constructor
• FillBoxWithMolecule() - new function to fill the remainder of the simulation box with some given filler molecules. Makes explicit use of the tesselated surfaces
• find_convex_border() - InsertStraddlingPoints() and CorrectConcaveBaselines() is called to correct for atoms outside the envelope and caused-by concave points
• Tesselation::InsertStraddlingPoints() enlarges the envelope for all atoms found outside, Tesselation::CorrectConcaveBaselines() corrects all found baselines if the adjacent triangles are concave by flipping.
• boundary.cpp: Lots of helper routines for stuff further below:
  • BoundaryLineSet::IsConnectedTo() checks whether lines have common endpoint
  • BoundaryLineSet::CheckConvexityCriterion() checks whether adjacent triangles are convex or concave
  • BoundaryLineSet::ContainsBoundaryPoint() checks whether line contains a given boundary point
  • BoundaryTriangleSet::ContainsBoundaryLine() and BoundaryTriangleSet::ContainsBoundaryPoint() check whether triangle contains boundary line or point
  • BoundaryTriangleSet::GetIntersectionInsideTriangle() calculates intersection point between line and triangle,
• The following routines are needed to check whether point is in- or outside:
  • Vector::GetIntersectionWithPlane() calculates intersection point of a plane and a line.
  • Vector::GetIntersectionOfTwoLinesOnPlane() intersection of two lines on the same plane.
• FIX: Tesselation::AddPoint() - newly created BoundaryPoint is removed if already present.

Problem: We want to associate a Tesselation class with each molecule class. However, so far we have to know about atoms and bond and molecules inside the Tesselation. We have to remove this dependency and create some intermediate class which enables/encapsulates the access to Vectors, e.g. hidden inside the atom class. This is also good OOP! The Tesselation also only needs a set of Vectors, not more!

File:

• src/molecules.cpp (modified) (1 diff)

src/molecules.cpp

@@ -120 +120 @@
 {
   if (pointer != NULL) {
-    atom *walker = new atom();
-    walker->type = pointer->type;  // copy element of atom
-    walker->x.CopyVector(&pointer->x); // copy coordination
-    walker->v.CopyVector(&pointer->v); // copy velocity
-    walker->FixedIon = pointer->FixedIon;
-    walker->sort = &walker->nr;
+    atom *walker = new atom(pointer);
+    walker->Name = (char *) Malloc(sizeof(char)*strlen(pointer->Name)+1, "atom::atom: *Name");
+    strcpy (walker->Name, pointer->Name);
     walker->nr = last_atom++;  // increase number within molecule
-    walker->father = pointer; //->GetTrueFather();
-    walker->Name = (char *) Malloc(sizeof(char)*strlen(pointer->Name)+1, "molecule::AddCopyAtom: *Name");
-    strcpy (walker->Name, pointer->Name);
     add(walker, end);
     if ((pointer->type != NULL) && (pointer->type->Z != 1))