Changeset 8f4df1 for src/tesselationhelpers.cpp

Timestamp:

Aug 7, 2010, 12:07:04 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, 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:

2d292d

Parents:

8d6d31 (diff), d74077 (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.

Message:

Merge branch 'AtomicPositionEncapsulation' into stable

Conflicts:

src/Actions/AtomAction/ChangeElementAction.cpp
src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp
src/Makefile.am
src/UIElements/TextUI/TextDialog.cpp
src/analysis_correlation.hpp
src/atom.cpp
src/atom_atominfo.hpp
src/bond.cpp
src/boundary.cpp
src/molecule_geometry.cpp
src/tesselation.cpp
src/tesselationhelpers.cpp
src/triangleintersectionlist.cpp
src/unittests/Makefile.am

• fixed #includes due to moves to Helpers and LinearAlgebra
• moved VectorInterface.* and vector_ops.* to LinearAlgebra
• no more direct access of atom::node, remapped to set/getPosition()
• no more direct access to atom::type, remapped to set/getType() (also in atom due to derivation and atominfo::AtomicElement is private not protected).

File:

• src/tesselationhelpers.cpp (modified) (19 diffs)

src/tesselationhelpers.cpp

@@ -10 +10 @@
 #include <fstream>
 
+#include "BoundaryLineSet.hpp"
+#include "BoundaryPointSet.hpp"
+#include "BoundaryPolygonSet.hpp"
+#include "BoundaryTriangleSet.hpp"
+#include "CandidateForTesselation.hpp"
 #include "Helpers/Info.hpp"
 #include "linkedcell.hpp"
@@ -18 +23 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "LinearAlgebra/Line.hpp"
-#include "vector_ops.hpp"
+#include "LinearAlgebra/vector_ops.hpp"
 #include "Helpers/Verbose.hpp"
 #include "LinearAlgebra/Plane.hpp"
@@ -144 +149 @@
  * \param *c third point
  */
-void GetCenterofCircumcircle(Vector * const Center, const Vector &a, const Vector &b, const Vector &c)
+void GetCenterofCircumcircle(Vector &Center, const Vector &a, const Vector &b, const Vector &c)
 {
         Info FunctionInfo(__func__);
@@ -156 +161 @@
   helper[2] = SideC.NormSquared()*(SideA.NormSquared()+SideB.NormSquared() - SideC.NormSquared());
 
-  Center->Zero();
-  *Center += helper[0] * a;
-  *Center += helper[1] * b;
-  *Center += helper[2] * c;
-  Center->Scale(1./(helper[0]+helper[1]+helper[2]));
-  Log() << Verbose(1) << "INFO: Center (2nd algo) is at " << *Center << "." << endl;
+  Center.Zero();
+  Center += helper[0] * a;
+  Center += helper[1] * b;
+  Center += helper[2] * c;
+  Center.Scale(1./(helper[0]+helper[1]+helper[2]));
+  Log() << Verbose(1) << "INFO: Center (2nd algo) is at " << Center << "." << endl;
 };
 
@@ -388 +393 @@
  * @return point which is second closest to the provided one
  */
-TesselPoint* FindSecondClosestTesselPoint(const Vector* Point, const LinkedCell* const LC)
+TesselPoint* FindSecondClosestTesselPoint(const Vector& Point, const LinkedCell* const LC)
 {
         Info FunctionInfo(__func__);
@@ -412 +417 @@
         if (List != NULL) {
           for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
-            helper = (*Point) - (*(*Runner)->node);
+            helper = (Point) - ((*Runner)->getPosition());
             double currentNorm = helper. Norm();
             if (currentNorm < distance) {
@@ -441 +446 @@
  * @return point which is closest to the provided one, NULL if none found
  */
-TesselPoint* FindClosestTesselPoint(const Vector* Point, TesselPoint *&SecondPoint, const LinkedCell* const LC)
+TesselPoint* FindClosestTesselPoint(const Vector& Point, TesselPoint *&SecondPoint, const LinkedCell* const LC)
 {
         Info FunctionInfo(__func__);
@@ -465 +470 @@
         if (List != NULL) {
           for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
-            helper = (*Point) - (*(*Runner)->node);
+            helper = (Point) - ((*Runner)->getPosition());
             double currentNorm = helper.NormSquared();
             if (currentNorm < distance) {
@@ -503 +508 @@
         Info FunctionInfo(__func__);
   // construct the plane of the two baselines (i.e. take both their directional vectors)
-  Vector Baseline = (*Base->endpoints[1]->node->node) - (*Base->endpoints[0]->node->node);
-  Vector OtherBaseline = (*OtherBase->endpoints[1]->node->node) - (*OtherBase->endpoints[0]->node->node);
+  Vector Baseline = (Base->endpoints[1]->node->getPosition()) - (Base->endpoints[0]->node->getPosition());
+  Vector OtherBaseline = (OtherBase->endpoints[1]->node->getPosition()) - (OtherBase->endpoints[0]->node->getPosition());
   Vector Normal = Baseline;
   Normal.VectorProduct(OtherBaseline);
@@ -511 +516 @@
 
   // project one offset point of OtherBase onto this plane (and add plane offset vector)
-  Vector NewOffset = (*OtherBase->endpoints[0]->node->node) - (*Base->endpoints[0]->node->node);
+  Vector NewOffset = (OtherBase->endpoints[0]->node->getPosition()) - (Base->endpoints[0]->node->getPosition());
   NewOffset.ProjectOntoPlane(Normal);
-  NewOffset += (*Base->endpoints[0]->node->node);
+  NewOffset += (Base->endpoints[0]->node->getPosition());
   Vector NewDirection = NewOffset + OtherBaseline;
 
   // calculate the intersection between this projected baseline and Base
   Vector *Intersection = new Vector;
-  Line line1 = makeLineThrough(*(Base->endpoints[0]->node->node),*(Base->endpoints[1]->node->node));
+  Line line1 = makeLineThrough((Base->endpoints[0]->node->getPosition()),(Base->endpoints[1]->node->getPosition()));
   Line line2 = makeLineThrough(NewOffset, NewDirection);
   *Intersection = line1.getIntersection(line2);
-  Normal = (*Intersection) - (*Base->endpoints[0]->node->node);
+  Normal = (*Intersection) - (Base->endpoints[0]->node->getPosition());
   DoLog(1) && (Log() << Verbose(1) << "Found closest point on " << *Base << " at " << *Intersection << ", factor in line is " << fabs(Normal.ScalarProduct(Baseline)/Baseline.NormSquared()) << "." << endl);
 
@@ -566 +571 @@
       *vrmlfile << "Sphere {" << endl << "  "; // 2 is sphere type
       for (i=0;i<NDIM;i++)
-        *vrmlfile << Walker->node->at(i)-center->at(i) << " ";
+        *vrmlfile << Walker->at(i)-center->at(i) << " ";
       *vrmlfile << "\t0.1\t1. 1. 1." << endl; // radius 0.05 and white as colour
       cloud->GoToNext();
@@ -576 +581 @@
       for (i=0;i<3;i++) { // print each node
         for (int j=0;j<NDIM;j++)  // and for each node all NDIM coordinates
-          *vrmlfile << TriangleRunner->second->endpoints[i]->node->node->at(j)-center->at(j) << " ";
+          *vrmlfile << TriangleRunner->second->endpoints[i]->node->at(j)-center->at(j) << " ";
         *vrmlfile << "\t";
       }
@@ -603 +608 @@
     Vector *center = cloud->GetCenter();
     // make the circumsphere's center absolute again
-    Vector helper = (1./3.) * ((*Tess->LastTriangle->endpoints[0]->node->node) +
-                               (*Tess->LastTriangle->endpoints[1]->node->node) +
-                               (*Tess->LastTriangle->endpoints[2]->node->node));
+    Vector helper = (1./3.) * ((Tess->LastTriangle->endpoints[0]->node->getPosition()) +
+                               (Tess->LastTriangle->endpoints[1]->node->getPosition()) +
+                               (Tess->LastTriangle->endpoints[2]->node->getPosition()));
     helper -= (*center);
     // and add to file plus translucency object
@@ -638 +643 @@
       *rasterfile << "2" << endl << "  ";  // 2 is sphere type
       for (int j=0;j<NDIM;j++) { // and for each node all NDIM coordinates
-        const double tmp = Walker->node->at(j)-center->at(j);
+        const double tmp = Walker->at(j)-center->at(j);
         *rasterfile << ((fabs(tmp) < MYEPSILON) ? 0 : tmp) << " ";
       }
@@ -651 +656 @@
       for (i=0;i<3;i++) {  // print each node
         for (int j=0;j<NDIM;j++) { // and for each node all NDIM coordinates
-          const double tmp = TriangleRunner->second->endpoints[i]->node->node->at(j)-center->at(j);
+          const double tmp = TriangleRunner->second->endpoints[i]->node->at(j)-center->at(j);
           *rasterfile << ((fabs(tmp) < MYEPSILON) ? 0 : tmp) << " ";
         }
@@ -705 +710 @@
       LookupList[Walker->nr] = Counter++;
       for (int i=0;i<NDIM;i++) {
-        const double tmp = Walker->node->at(i);
+        const double tmp = Walker->at(i);
         *tecplot << ((fabs(tmp) < MYEPSILON) ? 0 : tmp) << " ";
       }
@@ -754 +759 @@
     TriangleSet *triangles = TesselStruct->GetAllTriangles(PointRunner->second);
     for (TriangleSet::iterator TriangleRunner = triangles->begin(); TriangleRunner != triangles->end(); ++TriangleRunner) {
-      totalarea += CalculateAreaofGeneralTriangle(*(*TriangleRunner)->endpoints[0]->node->node, *(*TriangleRunner)->endpoints[1]->node->node, *(*TriangleRunner)->endpoints[2]->node->node);
+      totalarea += CalculateAreaofGeneralTriangle((*TriangleRunner)->endpoints[0]->node->getPosition() , (*TriangleRunner)->endpoints[1]->node->getPosition() , (*TriangleRunner)->endpoints[2]->node->getPosition());
     }
     ConcavityPerLine *= totalarea;
@@ -763 +768 @@
       line = (*TriangleRunner)->GetThirdLine(PointRunner->second);
       triangle = line->GetOtherTriangle(*TriangleRunner);
-      area = CalculateAreaofGeneralTriangle(*triangle->endpoints[0]->node->node, *triangle->endpoints[1]->node->node, *triangle->endpoints[2]->node->node);
-      area += CalculateAreaofGeneralTriangle(*(*TriangleRunner)->endpoints[0]->node->node, *(*TriangleRunner)->endpoints[1]->node->node, *(*TriangleRunner)->endpoints[2]->node->node);
+      area = CalculateAreaofGeneralTriangle(triangle->endpoints[0]->node->getPosition() , triangle->endpoints[1]->node->getPosition() , triangle->endpoints[2]->node->getPosition());
+      area += CalculateAreaofGeneralTriangle((*TriangleRunner)->endpoints[0]->node->getPosition() , (*TriangleRunner)->endpoints[1]->node->getPosition() , (*TriangleRunner)->endpoints[2]->node->getPosition());
       area *= -line->CalculateConvexity();
       if (area > 0)
@@ -797 +802 @@
     distance = 0.;
     for (TriangleMap::const_iterator TriangleRunner = Convex->TrianglesOnBoundary.begin(); TriangleRunner != Convex->TrianglesOnBoundary.end(); TriangleRunner++) {
-      const double CurrentDistance = Convex->GetDistanceSquaredToTriangle(*PointRunner->second->node->node, TriangleRunner->second);
+      const double CurrentDistance = Convex->GetDistanceSquaredToTriangle(PointRunner->second->node->getPosition() , TriangleRunner->second);
       if (CurrentDistance < distance)
         distance = CurrentDistance;