Changeset 9879f6 for src/boundary.cpp

Timestamp:

Mar 5, 2010, 10:16:47 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, 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:

d3347e

Parents:

e87acf

git-author:

Frederik Heber <heber@…> (03/05/10 10:08:44)

git-committer:

Frederik Heber <heber@…> (03/05/10 10:16:47)

Message:

Huge Refactoring due to class molecule now being an STL container.

• molecule::start and molecule::end were dropped. Hence, the usual construct Walker = start while (Walker->next != end) {

Walker = walker->next
...

}
was changed to
for (molecule::iterator iter = begin(); iter != end(); ++iter) {

...

}
and (*iter) used instead of Walker.

• Two build errors remain (beside some more in folder Actions, Patterns and unittest) in molecule_pointcloud.cpp and molecule.cpp
• lists.cpp was deleted as specialization of atom* was not needed anymore
• link, unlink, add, remove, removewithoutcheck all are not needed for atoms anymore, just for bonds (where first, last entries remain in molecule)
• CreateFatherLookupTable() was put back into class molecule.
• molecule::InternalPointer is now an iterator
• class PointCloud: GoToPrevious() and GetTerminalPoint() were dropped as not needed.
• some new STL functions in class molecule: size(), empty(), erase(), find() and insert()

File:

• src/boundary.cpp (modified) (11 diffs)

src/boundary.cpp

@@ -140 +140 @@
 {
         Info FunctionInfo(__func__);
-  atom *Walker = NULL;
   PointMap PointsOnBoundary;
   LineMap LinesOnBoundary;
@@ -166 +165 @@
 
     // 3b. construct set of all points, transformed into cylindrical system and with left and right neighbours
-    Walker = mol->start;
-    while (Walker->next != mol->end) {
-      Walker = Walker->next;
-      ProjectedVector.CopyVector(&Walker->x);
+    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+      ProjectedVector.CopyVector(&(*iter)->x);
       ProjectedVector.SubtractVector(MolCenter);
       ProjectedVector.ProjectOntoPlane(&AxisVector);
@@ -184 +181 @@
         angle = 2. * M_PI - angle;
       }
-      Log() << Verbose(1) << "Inserting " << *Walker << ": (r, alpha) = (" << radius << "," << angle << "): " << ProjectedVector << endl;
-      BoundaryTestPair = BoundaryPoints[axis].insert(BoundariesPair(angle, DistancePair (radius, Walker)));
+      Log() << Verbose(1) << "Inserting " << *(*iter) << ": (r, alpha) = (" << radius << "," << angle << "): " << ProjectedVector << endl;
+      BoundaryTestPair = BoundaryPoints[axis].insert(BoundariesPair(angle, DistancePair (radius, (*iter))));
       if (!BoundaryTestPair.second) { // same point exists, check first r, then distance of original vectors to center of gravity
         Log() << Verbose(2) << "Encountered two vectors whose projection onto axis " << axis << " is equal: " << endl;
         Log() << Verbose(2) << "Present vector: " << *BoundaryTestPair.first->second.second << endl;
-        Log() << Verbose(2) << "New vector: " << *Walker << endl;
+        Log() << Verbose(2) << "New vector: " << *(*iter) << endl;
         const double ProjectedVectorNorm = ProjectedVector.NormSquared();
         if ((ProjectedVectorNorm - BoundaryTestPair.first->second.first) > MYEPSILON) {
           BoundaryTestPair.first->second.first = ProjectedVectorNorm;
-          BoundaryTestPair.first->second.second = Walker;
+          BoundaryTestPair.first->second.second = (*iter);
           Log() << Verbose(2) << "Keeping new vector due to larger projected distance " << ProjectedVectorNorm << "." << endl;
         } else if (fabs(ProjectedVectorNorm - BoundaryTestPair.first->second.first) < MYEPSILON) {
-          helper.CopyVector(&Walker->x);
+          helper.CopyVector(&(*iter)->x);
           helper.SubtractVector(MolCenter);
           const double oldhelperNorm = helper.NormSquared();
@@ -202 +199 @@
           helper.SubtractVector(MolCenter);
           if (helper.NormSquared() < oldhelperNorm) {
-            BoundaryTestPair.first->second.second = Walker;
+            BoundaryTestPair.first->second.second = (*iter);
             Log() << Verbose(2) << "Keeping new vector due to larger distance to molecule center " << helper.NormSquared() << "." << endl;
           } else {
@@ -705 +702 @@
   int repetition[NDIM] = { 1, 1, 1 };
   int TotalNoClusters = 1;
-  atom *Walker = NULL;
   double totalmass = 0.;
   double clustervolume = 0.;
@@ -729 +725 @@
 
   // sum up the atomic masses
-  Walker = mol->start;
-  while (Walker->next != mol->end) {
-      Walker = Walker->next;
-      totalmass += Walker->type->mass;
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+      totalmass += (*iter)->type->mass;
   }
   Log() << Verbose(0) << "RESULT: The summed mass is " << setprecision(10) << totalmass << " atomicmassunit." << endl;
@@ -811 +805 @@
   Vector FillerDistance;
   double FillIt = false;
-  atom *Walker = NULL;
   bond *Binder = NULL;
   int i = 0;
@@ -884 +877 @@
 
           // go through all atoms
-          Walker = filler->start;
-          while (Walker->next != filler->end) {
-            Walker = Walker->next;
+          for (molecule::const_iterator iter = filler->begin(); iter != filler->end(); ++iter) {
             // copy atom ...
-            CopyAtoms[Walker->nr] = Walker->clone();
+            CopyAtoms[(*iter)->nr] = (*iter)->clone();
 
             // create atomic random translation vector ...
@@ -913 +904 @@
             // ... and put at new position
             if (DoRandomRotation)
-              CopyAtoms[Walker->nr]->x.MatrixMultiplication(Rotations);
-            CopyAtoms[Walker->nr]->x.AddVector(&AtomTranslations);
-            CopyAtoms[Walker->nr]->x.AddVector(&FillerTranslations);
-            CopyAtoms[Walker->nr]->x.AddVector(&CurrentPosition);
+              CopyAtoms[(*iter)->nr]->x.MatrixMultiplication(Rotations);
+            CopyAtoms[(*iter)->nr]->x.AddVector(&AtomTranslations);
+            CopyAtoms[(*iter)->nr]->x.AddVector(&FillerTranslations);
+            CopyAtoms[(*iter)->nr]->x.AddVector(&CurrentPosition);
 
             // insert into Filling
 
             // FIXME: gives completely different results if CopyAtoms[..] used instead of Walker, why???
-            Log() << Verbose(4) << "Filling atom " << *Walker << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[Walker->nr]->x) << "." << endl;
-            Filling->AddAtom(CopyAtoms[Walker->nr]);
+            Log() << Verbose(4) << "Filling atom " << *(*iter) << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[(*iter)->nr]->x) << "." << endl;
+            Filling->AddAtom(CopyAtoms[(*iter)->nr]);
           }
 
@@ -1036 +1027 @@
 //  // look whether all points are inside of the convex envelope, otherwise add them via degenerated triangles
 //  //->InsertStraddlingPoints(mol, LCList);
-//  mol->GoToFirst();
+//  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
 //  class TesselPoint *Runner = NULL;
-//  while (!mol->IsEnd()) {
-//    Runner = mol->GetPoint();
+//    Runner = *iter;
 //    Log() << Verbose(1) << "Checking on " << Runner->Name << " ... " << endl;
 //    if (!->IsInnerPoint(Runner, LCList)) {
@@ -1047 +1037 @@
 //      Log() << Verbose(2) << Runner->Name << " is inside of or on envelope." << endl;
 //    }
-//    mol->GoToNext();
 //  }