Changeset 34c43a for src/boundary.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, 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/boundary.cpp (modified) (14 diffs)

src/boundary.cpp

@@ -18 +18 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "BoundaryPointSet.hpp"
-#include "BoundaryLineSet.hpp"
-#include "BoundaryTriangleSet.hpp"
-#include "CandidateForTesselation.hpp"
-//#include "TesselPoint.hpp"
-#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
 #include "boundary.hpp"
+#include "BoundaryLineSet.hpp"
+#include "BoundaryPointSet.hpp"
+#include "BoundaryTriangleSet.hpp"
+#include "Box.hpp"
+#include "CandidateForTesselation.hpp"
+#include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
 #include "element.hpp"
 #include "Helpers/helpers.hpp"
-#include "CodePatterns/Info.hpp"
+#include "LinearAlgebra/Plane.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "linkedcell.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
+#include "PointCloudAdaptor.hpp"
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
+#include "RandomNumbers/RandomNumberGenerator.hpp"
 #include "tesselation.hpp"
 #include "tesselationhelpers.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/Plane.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
-#include "RandomNumbers/RandomNumberGenerator.hpp"
-#include "Box.hpp"
 
 #include <iostream>
@@ -378 +377 @@
 
   // 3b. go through all lines, that are not yet part of two triangles (only of one so far)
-  TesselStruct->TesselateOnBoundary(mol);
+  PointCloudAdaptor< molecule > cloud(const_cast<molecule *>(mol));
+  TesselStruct->TesselateOnBoundary(cloud);
 
   // 3c. check whether all atoms lay inside the boundary, if not, add to boundary points, segment triangle into three with the new point
-  if (!TesselStruct->InsertStraddlingPoints(mol, LCList))
+  if (!TesselStruct->InsertStraddlingPoints(cloud, LCList))
     DoeLog(1) && (eLog()<< Verbose(1) << "Insertion of straddling points failed!" << endl);
 
@@ -645 +645 @@
 {
         Info FunctionInfo(__func__);
+  PointCloudAdaptor< molecule > cloud(const_cast<molecule *>(mol));
   // 4. Store triangles in tecplot file
   if (filename != NULL) {
@@ -652 +653 @@
       OutputName.append(TecplotSuffix);
       ofstream *tecplot = new ofstream(OutputName.c_str());
-      WriteTecplotFile(tecplot, TesselStruct, mol, -1);
+      WriteTecplotFile(tecplot, TesselStruct, cloud, -1);
       tecplot->close();
       delete(tecplot);
@@ -661 +662 @@
       OutputName.append(Raster3DSuffix);
       ofstream *rasterplot = new ofstream(OutputName.c_str());
-      WriteRaster3dFile(rasterplot, TesselStruct, mol);
+      WriteRaster3dFile(rasterplot, TesselStruct, cloud);
       rasterplot->close();
       delete(rasterplot);
@@ -699 +700 @@
   BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
   GreatestDiameter = GetDiametersOfCluster(BoundaryPoints, mol, TesselStruct, IsAngstroem);
-  LinkedCell *LCList = new LinkedCell(*mol, 10.);
+  PointCloudAdaptor< molecule > cloud(mol);
+  LinkedCell *LCList = new LinkedCell(cloud, 10.);
   FindConvexBorder(mol, BoundaryPoints, TesselStruct, (const LinkedCell *&)LCList, NULL);
   delete (LCList);
@@ -808 +810 @@
     if ((*ListRunner)->getAtomCount() > 0) {
       DoLog(1) && (Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl);
-      LCList[(*ListRunner)] = new LinkedCell(*(*ListRunner), 10.); // get linked cell list
+      PointCloudAdaptor< molecule > cloud(*ListRunner);
+      LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
       DoLog(1) && (Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl);
       TesselStruct[(*ListRunner)] = NULL;
@@ -1015 +1018 @@
 {
   size_t compareTo = 0;
-  LinkedCell::LinkedNodes* liste = LC->GetPointsInsideSphere(boundary == 0. ? MYEPSILON : boundary, &CurrentPosition);
+  TesselPointSTLList* liste = LC->GetPointsInsideSphere(boundary == 0. ? MYEPSILON : boundary, &CurrentPosition);
   if (filler != NULL) {
-    for (LinkedCell::LinkedNodes::const_iterator iter = liste->begin();
+    for (TesselPointSTLList::const_iterator iter = liste->begin();
         iter != liste->end();
         ++iter) {
@@ -1031 +1034 @@
   if (!result) {
     DoLog(0) && (Log() << Verbose(0) << "Skipping because of the following atoms:" << std::endl);
-    for (LinkedCell::LinkedNodes::const_iterator iter = liste->begin();
+    for (TesselPointSTLList::const_iterator iter = liste->begin();
         iter != liste->end();
         ++iter) {
@@ -1084 +1087 @@
     if ((*ListRunner)->getAtomCount() > 0) {
       DoLog(1) && (Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl);
-      LCList[(*ListRunner)] = new LinkedCell(*(*ListRunner), 10.); // get linked cell list
+      PointCloudAdaptor< molecule > cloud(*ListRunner);
+      LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
     }
 
@@ -1215 +1219 @@
  * \return true - tesselation successful, false - tesselation failed
  */
-bool FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
+bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
 {
         Info FunctionInfo(__func__);
@@ -1236 +1240 @@
 
   // initialise Linked Cell
+  PointCloudAdaptor< molecule > cloud(mol);
   if (LCList == NULL) {
-    LCList = new LinkedCell(*mol, 2.*RADIUS);
+    LCList = new LinkedCell(cloud, 2.*RADIUS);
     freeLC = true;
   }
@@ -1248 +1253 @@
   if (filename != NULL) {
     if ((DoSingleStepOutput && ((TesselStruct->TrianglesOnBoundary.size() % SingleStepWidth == 0)))) { // if we have a new triangle and want to output each new triangle configuration
-      TesselStruct->Output(filename, mol);
+      TesselStruct->Output(filename, cloud);
     }
   }
@@ -1288 +1293 @@
     if (filename != NULL) {
       if ((DoSingleStepOutput && ((TesselStruct->TrianglesOnBoundary.size() % SingleStepWidth == 0)))) { // if we have a new triangle and want to output each new triangle configuration
-        TesselStruct->Output(filename, mol);
+        TesselStruct->Output(filename, cloud);
       }
     }