Changeset 1024cb for src/boundary.cpp

Timestamp:

May 31, 2010, 5:32:27 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, 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:

e08c46

Parents:

42af9e (diff), a7b761b (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.

git-author:

Frederik Heber <heber@…> (05/31/10 17:29:30)

git-committer:

Frederik Heber <heber@…> (05/31/10 17:32:27)

Message:

Merge commit 'jupiter/MoleculeStartEndSwitch' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp
molecuilder/src/unittests/listofbondsunittest.cpp

Integration of MoleculeStartEndSwitch had the following consequences:

• no more AtomCount -> getAtomCount()
• no more start/end -> begin(), end() and iterator
• no more decent ordering in atomic ids (hence, Simple_configuration/8 and Domain/5, Domain/6 now check by comparing sorted xyz, not confs)

There is still a huge problem with bonds. One test runs into an endless loop.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/boundary.cpp (modified) (17 diffs)

src/boundary.cpp

@@ -139 +139 @@
 {
         Info FunctionInfo(__func__);
-  atom *Walker = NULL;
   PointMap PointsOnBoundary;
   LineMap LinesOnBoundary;
@@ -165 +164 @@
 
     // 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 = Walker->x - (*MolCenter);
+    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+      ProjectedVector = (*iter)->x - (*MolCenter);
       ProjectedVector.ProjectOntoPlane(AxisVector);
 
@@ -182 +179 @@
         angle = 2. * M_PI - angle;
       }
-      DoLog(1) && (Log() << Verbose(1) << "Inserting " << *Walker << ": (r, alpha) = (" << radius << "," << angle << "): " << ProjectedVector << endl);
-      BoundaryTestPair = BoundaryPoints[axis].insert(BoundariesPair(angle, DistancePair (radius, Walker)));
+    DoLog(1) && (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
         DoLog(2) && (Log() << Verbose(2) << "Encountered two vectors whose projection onto axis " << axis << " is equal: " << endl);
         DoLog(2) && (Log() << Verbose(2) << "Present vector: " << *BoundaryTestPair.first->second.second << endl);
-        DoLog(2) && (Log() << Verbose(2) << "New vector: " << *Walker << endl);
+        DoLog(2) && (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);
           DoLog(2) && (Log() << Verbose(2) << "Keeping new vector due to larger projected distance " << ProjectedVectorNorm << "." << endl);
         } else if (fabs(ProjectedVectorNorm - BoundaryTestPair.first->second.first) < MYEPSILON) {
-          helper = Walker->x - (*MolCenter);
+          helper = (*iter)->x;
+          helper -= *MolCenter;
           const double oldhelperNorm = helper.NormSquared();
           helper = BoundaryTestPair.first->second.second->x - (*MolCenter);
           if (helper.NormSquared() < oldhelperNorm) {
-            BoundaryTestPair.first->second.second = Walker;
+            BoundaryTestPair.first->second.second = (*iter);
             DoLog(2) && (Log() << Verbose(2) << "Keeping new vector due to larger distance to molecule center " << helper.NormSquared() << "." << endl);
           } else {
@@ -620 +618 @@
   for (TriangleMap::iterator runner = TesselStruct->TrianglesOnBoundary.begin(); runner != TesselStruct->TrianglesOnBoundary.end(); runner++)
     { // go through every triangle, calculate volume of its pyramid with CoG as peak
-      x = (*runner->second->endpoints[0]->node->node) - (*runner->second->endpoints[1]->node->node);
-      y = (*runner->second->endpoints[0]->node->node) - (*runner->second->endpoints[2]->node->node);
-      const double a = sqrt(runner->second->endpoints[0]->node->node->DistanceSquared(*runner->second->endpoints[1]->node->node));
-      const double b = sqrt(runner->second->endpoints[0]->node->node->DistanceSquared(*runner->second->endpoints[2]->node->node));
-      const double c = sqrt(runner->second->endpoints[2]->node->node->DistanceSquared(*runner->second->endpoints[1]->node->node));
+      x = runner->second->getEndpoint(0) - runner->second->getEndpoint(1);
+      y = runner->second->getEndpoint(0) - runner->second->getEndpoint(2);
+      const double a = x.Norm();
+      const double b = y.Norm();
+      const double c = runner->second->getEndpoint(2).distance(runner->second->getEndpoint(1));
       const double G = sqrt(((a + b + c) * (a + b + c) - 2 * (a * a + b * b + c * c)) / 16.); // area of tesselated triangle
-      x = Plane(*(runner->second->endpoints[0]->node->node),
-                *(runner->second->endpoints[1]->node->node),
-                *(runner->second->endpoints[2]->node->node)).getNormal();
-      x.Scale(runner->second->endpoints[1]->node->node->ScalarProduct(x));
+      x = runner->second->getPlane().getNormal();
+      x.Scale(runner->second->getEndpoint(1).ScalarProduct(x));
       const double h = x.Norm(); // distance of CoG to triangle
       const double PyramidVolume = (1. / 3.) * G * h; // this formula holds for _all_ pyramids (independent of n-edge base or (not) centered peak)
@@ -697 +693 @@
   int repetition[NDIM] = { 1, 1, 1 };
   int TotalNoClusters = 1;
-  atom *Walker = NULL;
   double totalmass = 0.;
   double clustervolume = 0.;
@@ -721 +716 @@
 
   // 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;
   }
   DoLog(0) && (Log() << Verbose(0) << "RESULT: The summed mass is " << setprecision(10) << totalmass << " atomicmassunit." << endl);
@@ -806 +799 @@
   Vector Inserter;
   double FillIt = false;
-  atom *Walker = NULL;
   bond *Binder = NULL;
   double phi[NDIM];
@@ -813 +805 @@
 
   for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++)
-    if ((*ListRunner)->AtomCount > 0) {
+    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
@@ -831 +823 @@
   }
 
-  filler->CountAtoms();
-  atom * CopyAtoms[filler->AtomCount];
+  atom * CopyAtoms[filler->getAtomCount()];
 
   // calculate filler grid in [0,1]^3
@@ -857 +848 @@
 
         // go through all atoms
-        for (int i=0;i<filler->AtomCount;i++)
+        for (int i=0;i<filler->getAtomCount();i++)
           CopyAtoms[i] = NULL;
-        Walker = filler->start;
-        while (Walker->next != filler->end) {
-          Walker = Walker->next;
+        for(molecule::iterator iter = filler->begin(); iter !=filler->end();++filler){
 
           // create atomic random translation vector ...
@@ -885 +874 @@
 
           // ... and put at new position
-          Inserter = Walker->x;
+          Inserter = (*iter)->x;
           if (DoRandomRotation)
             Inserter.MatrixMultiplication(Rotations);
@@ -909 +898 @@
             DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is outer point." << endl);
             // copy atom ...
-            CopyAtoms[Walker->nr] = Walker->clone();
-            CopyAtoms[Walker->nr]->x = Inserter;
-            Filling->AddAtom(CopyAtoms[Walker->nr]);
-            DoLog(4) && (Log() << Verbose(4) << "Filling atom " << *Walker << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[Walker->nr]->x) << "." << endl);
+            CopyAtoms[(*iter)->nr] = (*iter)->clone();
+            CopyAtoms[(*iter)->nr]->x = Inserter;
+            Filling->AddAtom(CopyAtoms[(*iter)->nr]);
+            DoLog(4) && (Log() << Verbose(4) << "Filling atom " << **iter << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[(*iter)->nr]->x) << "." << endl);
           } else {
             DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is inner point, within boundary or outside of MaxDistance." << endl);
-            CopyAtoms[Walker->nr] = NULL;
+            CopyAtoms[(*iter)->nr] = NULL;
             continue;
           }
@@ -954 +943 @@
   bool TesselationFailFlag = false;
 
+  mol->getAtomCount();
+
   if (TesselStruct == NULL) {
     DoLog(1) && (Log() << Verbose(1) << "Allocating Tesselation struct ..." << endl);
@@ -1025 +1016 @@
 //  // 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)) {
@@ -1036 +1026 @@
 //      Log() << Verbose(2) << Runner->Name << " is inside of or on envelope." << endl;
 //    }
-//    mol->GoToNext();
 //  }
 
@@ -1045 +1034 @@
   status = CheckListOfBaselines(TesselStruct);
 
+  cout << "before correction" << endl;
+
   // store before correction
-  StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, "");
+  StoreTrianglesinFile(mol, TesselStruct, filename, "");
 
 //  // correct degenerated polygons
@@ -1056 +1047 @@
   // write final envelope
   CalculateConcavityPerBoundaryPoint(TesselStruct);
-  StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, "");
+  cout << "after correction" << endl;
+  StoreTrianglesinFile(mol, TesselStruct, filename, "");
 
   if (freeLC)