Changeset 34c43a for src/Actions

Timestamp:

Mar 1, 2011, 10:16:38 AM (14 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:

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.

Location:

src/Actions

Files:

• AnalysisAction/MolecularVolumeAction.cpp (modified) (2 diffs)
• AnalysisAction/SurfaceCorrelationAction.cpp (modified) (3 diffs)
• FragmentationAction/ConstructBondGraphAction.cpp (modified) (5 diffs)
• TesselationAction/ConvexEnvelopeAction.cpp (modified) (2 diffs)
• TesselationAction/NonConvexEnvelopeAction.cpp (modified) (2 diffs)

src/Actions/AnalysisAction/MolecularVolumeAction.cpp

@@ -26 +26 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "PointCloudAdaptor.hpp"
 #include "tesselation.hpp"
 #include "World.hpp"
@@ -51 +52 @@
     const LinkedCell *LCList = NULL;
     DoLog(0) && (Log() << Verbose(0) << "Evaluating volume of the convex envelope.");
-    LCList = new LinkedCell(*mol, 10.);
+    PointCloudAdaptor< molecule > cloud(mol);
+    LCList = new LinkedCell(cloud, 10.);
     config * const configuration = World::getInstance().getConfig();
     //Boundaries *BoundaryPoints = NULL;

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -25 +25 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "element.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"
+#include "PointCloudAdaptor.hpp"
 #include "tesselation.hpp"
-#include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
 
@@ -57 +59 @@
   output.open(params.outputname.string().c_str());
   binoutput.open(params.binoutputname.string().c_str());
-  ASSERT(params.Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
+  molecule *surfacemol = const_cast<molecule *>(params.Boundary);
+  ASSERT(surfacemol != NULL, "No molecule specified for SurfaceCorrelation.");
   const double radius = 4.;
   double LCWidth = 20.;
@@ -73 +76 @@
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
-  LCList = new LinkedCell(*params.Boundary, LCWidth);
-  FindNonConvexBorder(params.Boundary, TesselStruct, LCList, radius, NULL);
+  PointCloudAdaptor<molecule> cloud(surfacemol);
+  LCList = new LinkedCell(cloud, LCWidth);
+  FindNonConvexBorder(surfacemol, TesselStruct, LCList, radius, NULL);
   CorrelationToSurfaceMap *surfacemap = NULL;
   if (params.periodic)

src/Actions/FragmentationAction/ConstructBondGraphAction.cpp

@@ -26 +26 @@
 #include "bond.hpp"
 #include "bondgraph.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
 #include "linkedcell.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "molecule.hpp"
+#include "PointCloudAdaptor.hpp"
 #include "World.hpp"
 #include "WorldTime.hpp"
 
 #include <iostream>
+#include <list>
 #include <string>
 
@@ -86 +88 @@
   if ((AtomCount > 1) && (BondDistance > 1.)) {
     DoLog(2) && (Log() << Verbose(2) << "Creating Linked Cell structure ... " << endl);
-    LinkedCell::LinkedNodes list;
+    TesselPointSTLList list;
     for (World::AtomSelectionIterator AtomRunner = World::getInstance().beginAtomSelection();
         AtomRunner != World::getInstance().endAtomSelection();
@@ -92 +94 @@
       list.push_back(AtomRunner->second);
     }
-    LC = new LinkedCell(list, BondDistance);
+    PointCloudAdaptor< TesselPointSTLList > cloud(&list);
+    LC = new LinkedCell(cloud, BondDistance);
 
     // create a list to map Tesselpoint::nr to atom *
@@ -111 +114 @@
       for (LC->n[1] = 0; LC->n[1] < LC->N[1]; LC->n[1]++)
         for (LC->n[2] = 0; LC->n[2] < LC->N[2]; LC->n[2]++) {
-          const LinkedCell::LinkedNodes *List = LC->GetCurrentCell();
+          const TesselPointSTLList *List = LC->GetCurrentCell();
 //          Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
           if (List != NULL) {
-            for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin();
+            for (TesselPointSTLList::const_iterator Runner = List->begin();
                 Runner != List->end();
                 Runner++) {
@@ -124 +127 @@
                 for (n[1] = -1; n[1] <= 1; n[1]++)
                   for (n[2] = -1; n[2] <= 1; n[2]++) {
-                    const LinkedCell::LinkedNodes *OtherList = LC->GetRelativeToCurrentCell(n);
+                    const TesselPointSTLList *OtherList = LC->GetRelativeToCurrentCell(n);
 //                    Log() << Verbose(2) << "Current relative cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
                     if (OtherList != NULL) {
-                      for (LinkedCell::LinkedNodes::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
+                      for (TesselPointSTLList::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
                         if (AtomIds.find(*OtherRunner)->second > AtomIds.find(Walker)->second) {
                           OtherWalker = dynamic_cast<atom*>(*OtherRunner);

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -21 +21 @@
 
 #include "boundary.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
 #include "linkedcell.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
+#include "PointCloudAdaptor.hpp"
 #include "tesselation.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "World.hpp"
 
@@ -55 +56 @@
     DoLog(1) && (Log() << Verbose(1) << "Storing tecplot convex data in " << params.filenameConvex << "." << endl);
     DoLog(1) && (Log() << Verbose(1) << "Storing tecplot non-convex data in " << params.filenameNonConvex << "." << endl);
-    LCList = new LinkedCell(*mol, 100.);
+    PointCloudAdaptor<molecule> cloud(mol);
+    LCList = new LinkedCell(cloud, 100.);
     //Boundaries *BoundaryPoints = NULL;
     //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);

src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

@@ -21 +21 @@
 
 #include "boundary.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "linkedcell.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
+#include "PointCloudAdaptor.hpp"
 #include "tesselation.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "World.hpp"
 
@@ -55 +56 @@
     DoLog(1) && (Log() << Verbose(1) << "Specified molecule has " << Boundary->getAtomCount() << " atoms." << endl);
     start = clock();
-    LCList = new LinkedCell(*Boundary, params.SphereRadius*2.);
+    PointCloudAdaptor< molecule > cloud(Boundary);
+    LCList = new LinkedCell(cloud, params.SphereRadius*2.);
     Success = FindNonConvexBorder(Boundary, T, LCList, params.SphereRadius, params.filename.string().c_str());
     //FindDistributionOfEllipsoids(T, &LCList, N, number, params.filename.c_str());