Changeset 34c43a for src/tesselationhelpers.cpp

Timestamp:

Mar 1, 2011, 10:16:38 AM (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, Candidate_v1.7.1, 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:

caa06ef

Parents:

ba5215

git-author:

Frederik Heber <heber@…> (02/21/11 18:02:41)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

Bigger change: Replaced PointCloud by PointCloudAdaptor.

• PointCloud is no more inherited by classes molecule and Tesselation but an interface to an (templated) adaptor called PointCloudAdaptor.
• As BoundaryPointSet only wraps TesselPoint member, we needed
• use CodePatterns/IteratorAdaptors.hpp to access the value (TesselPoint*) in the map Tesselation::BoundaryPointSet, requiring now v1.0.11.
• lots of places in Actions, Tesselation, and boundary had to be adapted to the new PointCloudAdaptor.
• LinkedCell also now only has constructor requesting a IPointCloud structure.
• this all will make BondGraph construction a lot easier (note that World has map containing atoms, where molecule has list. Hence, we need this IteratorAdaptor).
• TESTFIX: Marked Tesselation/Convex, Tesselation/NonConvex, and Tesselation/BigNonConvex as expected to fail due to wrong name in teecplot file. This is gonna be fixed in next issue.

File:

• src/tesselationhelpers.cpp (modified) (14 diffs)

src/tesselationhelpers.cpp

@@ -28 +28 @@
 #include "CandidateForTesselation.hpp"
 #include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "IPointCloud.hpp"
+#include "LinearAlgebra/Line.hpp"
+#include "LinearAlgebra/LinearSystemOfEquations.hpp"
+#include "LinearAlgebra/Plane.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
+#include "LinearAlgebra/Vector.hpp"
+#include "LinearAlgebra/vector_ops.hpp"
 #include "linkedcell.hpp"
-#include "LinearAlgebra/LinearSystemOfEquations.hpp"
-#include "CodePatterns/Log.hpp"
 #include "tesselation.hpp"
 #include "tesselationhelpers.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "LinearAlgebra/Line.hpp"
-#include "LinearAlgebra/vector_ops.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "LinearAlgebra/Plane.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
 
 void GetSphere(Vector * const center, const Vector &a, const Vector &b, const Vector &c, const double RADIUS)
@@ -427 +428 @@
     for (LC->n[1] = Nlower[1]; LC->n[1] <= Nupper[1]; LC->n[1]++)
       for (LC->n[2] = Nlower[2]; LC->n[2] <= Nupper[2]; LC->n[2]++) {
-        const LinkedCell::LinkedNodes *List = LC->GetCurrentCell();
+        const TesselPointSTLList *List = LC->GetCurrentCell();
         //Log() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << endl;
         if (List != NULL) {
-          for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
+          for (TesselPointSTLList::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
             helper = (Point) - ((*Runner)->getPosition());
             double currentNorm = helper. Norm();
@@ -480 +481 @@
     for (LC->n[1] = Nlower[1]; LC->n[1] <= Nupper[1]; LC->n[1]++)
       for (LC->n[2] = Nlower[2]; LC->n[2] <= Nupper[2]; LC->n[2]++) {
-        const LinkedCell::LinkedNodes *List = LC->GetCurrentCell();
+        const TesselPointSTLList *List = LC->GetCurrentCell();
         //Log() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << endl;
         if (List != NULL) {
-          for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
+          for (TesselPointSTLList::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
             helper = (Point) - ((*Runner)->getPosition());
             double currentNorm = helper.NormSquared();
@@ -569 +570 @@
  * \param *mol molecule structure with atom positions
  */
-void WriteVrmlFile(ofstream * const vrmlfile, const Tesselation * const Tess, const PointCloud * const cloud)
+void WriteVrmlFile(ofstream * const vrmlfile, const Tesselation * const Tess, IPointCloud & cloud)
 {
         Info FunctionInfo(__func__);
   TesselPoint *Walker = NULL;
   int i;
-  Vector *center = cloud->GetCenter();
+  Vector *center = cloud.GetCenter();
   if (vrmlfile != NULL) {
     //Log() << Verbose(1) << "Writing Raster3D file ... ";
@@ -580 +581 @@
     *vrmlfile << "#Created by molecuilder" << endl;
     *vrmlfile << "#All atoms as spheres" << endl;
-    cloud->GoToFirst();
-    while (!cloud->IsEnd()) {
-      Walker = cloud->GetPoint();
+    cloud.GoToFirst();
+    while (!cloud.IsEnd()) {
+      Walker = cloud.GetPoint();
       *vrmlfile << "Sphere {" << endl << "  "; // 2 is sphere type
       for (i=0;i<NDIM;i++)
         *vrmlfile << Walker->at(i)-center->at(i) << " ";
       *vrmlfile << "\t0.1\t1. 1. 1." << endl; // radius 0.05 and white as colour
-      cloud->GoToNext();
+      cloud.GoToNext();
     }
 
@@ -613 +614 @@
  * \param *mol molecule structure with atom positions
  */
-void IncludeSphereinRaster3D(ofstream * const rasterfile, const Tesselation * const Tess, const PointCloud * const cloud)
+void IncludeSphereinRaster3D(ofstream * const rasterfile, const Tesselation * const Tess, IPointCloud & cloud)
 {
         Info FunctionInfo(__func__);
@@ -620 +621 @@
   if (Tess->LastTriangle != NULL) {
     // include the current position of the virtual sphere in the temporary raster3d file
-    Vector *center = cloud->GetCenter();
+    Vector *center = cloud.GetCenter();
     // make the circumsphere's center absolute again
     Vector helper = (1./3.) * ((Tess->LastTriangle->endpoints[0]->node->getPosition()) +
@@ -641 +642 @@
  * \param *mol molecule structure with atom positions
  */
-void WriteRaster3dFile(ofstream * const rasterfile, const Tesselation * const Tess, const PointCloud * const cloud)
+void WriteRaster3dFile(ofstream * const rasterfile, const Tesselation * const Tess, IPointCloud & cloud)
 {
         Info FunctionInfo(__func__);
   TesselPoint *Walker = NULL;
   int i;
-  Vector *center = cloud->GetCenter();
+  Vector *center = cloud.GetCenter();
   if (rasterfile != NULL) {
     //Log() << Verbose(1) << "Writing Raster3D file ... ";
@@ -652 +653 @@
     *rasterfile << "@header.r3d" << endl;
     *rasterfile << "# All atoms as spheres" << endl;
-    cloud->GoToFirst();
-    while (!cloud->IsEnd()) {
-      Walker = cloud->GetPoint();
+    cloud.GoToFirst();
+    while (!cloud.IsEnd()) {
+      Walker = cloud.GetPoint();
       *rasterfile << "2" << endl << "  ";  // 2 is sphere type
       for (int j=0;j<NDIM;j++) { // and for each node all NDIM coordinates
@@ -661 +662 @@
       }
       *rasterfile << "\t0.1\t1. 1. 1." << endl; // radius 0.05 and white as colour
-      cloud->GoToNext();
+      cloud.GoToNext();
     }
 
@@ -691 +692 @@
  * \param N arbitrary number to differentiate various zones in the tecplot format
  */
-void WriteTecplotFile(ofstream * const tecplot, const Tesselation * const TesselStruct, const PointCloud * const cloud, const int N)
+void WriteTecplotFile(ofstream * const tecplot, const Tesselation * const TesselStruct, IPointCloud & cloud, const int N)
 {
         Info FunctionInfo(__func__);
@@ -700 +701 @@
     *tecplot << "ZONE T=\"";
     if (N < 0) {
-      *tecplot << cloud->GetName();
+      *tecplot << cloud.GetName();
     } else {
       *tecplot << N << "-";
@@ -711 +712 @@
     }
     *tecplot << "\", N=" << TesselStruct->PointsOnBoundary.size() << ", E=" << TesselStruct->TrianglesOnBoundary.size() << ", DATAPACKING=POINT, ZONETYPE=FETRIANGLE" << endl;
-    const int MaxId=cloud->GetMaxId();
-    int *LookupList = new int[MaxId];
-    for (int i=0; i< MaxId ; i++){
+    const int MaxId=cloud.GetMaxId();
+    ASSERT(MaxId >= 0, "WriteTecplotFile() - negative MaxId? No atoms present?");
+    int *LookupList = new int[MaxId+1];
+    for (int i=0; i<= MaxId ; i++){
       LookupList[i] = -1;
     }
@@ -722 +724 @@
     for (PointMap::const_iterator target = TesselStruct->PointsOnBoundary.begin(); target != TesselStruct->PointsOnBoundary.end(); ++target) {
       Walker = target->second->node;
+      ASSERT(Walker->nr <= MaxId, "WriteTecplotFile() - Id of particle greater than MaxId.");
       LookupList[Walker->nr] = Counter++;
       for (int i=0;i<NDIM;i++) {