Changeset 8f4df1 for src/boundary.cpp

Timestamp:

Aug 7, 2010, 12:07:04 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:

2d292d

Parents:

8d6d31 (diff), d74077 (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.

Message:

Merge branch 'AtomicPositionEncapsulation' into stable

Conflicts:

src/Actions/AtomAction/ChangeElementAction.cpp
src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp
src/Makefile.am
src/UIElements/TextUI/TextDialog.cpp
src/analysis_correlation.hpp
src/atom.cpp
src/atom_atominfo.hpp
src/bond.cpp
src/boundary.cpp
src/molecule_geometry.cpp
src/tesselation.cpp
src/tesselationhelpers.cpp
src/triangleintersectionlist.cpp
src/unittests/Makefile.am

• fixed #includes due to moves to Helpers and LinearAlgebra
• moved VectorInterface.* and vector_ops.* to LinearAlgebra
• no more direct access of atom::node, remapped to set/getPosition()
• no more direct access to atom::type, remapped to set/getType() (also in atom due to derivation and atominfo::AtomicElement is private not protected).

File:

• src/boundary.cpp (modified) (10 diffs)

src/boundary.cpp

@@ -7 +7 @@
 
 #include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
+#include "BoundaryPointSet.hpp"
+#include "BoundaryLineSet.hpp"
+#include "BoundaryTriangleSet.hpp"
+#include "CandidateForTesselation.hpp"
+//#include "TesselPoint.hpp"
 #include "World.hpp"
 #include "atom.hpp"
@@ -87 +92 @@
               if (Neighbour == BoundaryPoints[axis].end()) // make it wrap around
                 Neighbour = BoundaryPoints[axis].begin();
-              DistanceVector = runner->second.second->x - Neighbour->second.second->x;
+              DistanceVector = (runner->second.second->getPosition()) - (Neighbour->second.second->getPosition());
               do { // seek for neighbour pair where it flips
                   OldComponent = DistanceVector[Othercomponent];
@@ -93 +98 @@
                   if (Neighbour == BoundaryPoints[axis].end()) // make it wrap around
                     Neighbour = BoundaryPoints[axis].begin();
-                  DistanceVector = runner->second.second->x - Neighbour->second.second->x;
+                  DistanceVector = (runner->second.second->getPosition()) - (Neighbour->second.second->getPosition());
                   //Log() << Verbose(2) << "OldComponent is " << OldComponent << ", new one is " << DistanceVector.x[Othercomponent] << "." << endl;
                 } while ((runner != Neighbour) && (fabs(OldComponent / fabs(
@@ -105 +110 @@
                   //Log() << Verbose(1) << "The pair, where the sign of OtherComponent flips, is: " << *(Neighbour->second.second) << " and " << *(OtherNeighbour->second.second) << "." << endl;
                   // now we have found the pair: Neighbour and OtherNeighbour
-                  OtherVector = runner->second.second->x - OtherNeighbour->second.second->x;
+                  OtherVector = (runner->second.second->getPosition()) - (OtherNeighbour->second.second->getPosition());
                   //Log() << Verbose(1) << "Distances to Neighbour and OtherNeighbour are " << DistanceVector.x[component] << " and " << OtherVector.x[component] << "." << endl;
                   //Log() << Verbose(1) << "OtherComponents to Neighbour and OtherNeighbour are " << DistanceVector.x[Othercomponent] << " and " << OtherVector.x[Othercomponent] << "." << endl;
@@ -173 +178 @@
     // 3b. construct set of all points, transformed into cylindrical system and with left and right neighbours
     for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      ProjectedVector = (*iter)->x - (*MolCenter);
+      ProjectedVector = (*iter)->getPosition() - (*MolCenter);
       ProjectedVector.ProjectOntoPlane(AxisVector);
 
@@ -199 +204 @@
           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 = (*iter)->x;
-          helper -= *MolCenter;
+          helper = (*iter)->getPosition() - (*MolCenter);
           const double oldhelperNorm = helper.NormSquared();
-          helper = BoundaryTestPair.first->second.second->x - (*MolCenter);
+          helper = BoundaryTestPair.first->second.second->getPosition() - (*MolCenter);
           if (helper.NormSquared() < oldhelperNorm) {
             BoundaryTestPair.first->second.second = (*iter);
@@ -255 +259 @@
         {
           Vector SideA, SideB, SideC, SideH;
-          SideA = left->second.second->x - (*MolCenter);
+          SideA = left->second.second->getPosition() - (*MolCenter);
           SideA.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideA: " << SideA << endl;
 
-          SideB = right->second.second->x -(*MolCenter);
+          SideB = right->second.second->getPosition() -(*MolCenter);
           SideB.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideB: " << SideB << endl;
 
-          SideC = left->second.second->x - right->second.second->x;
+          SideC = left->second.second->getPosition() - right->second.second->getPosition();
           SideC.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideC: " << SideC << endl;
 
-          SideH = runner->second.second->x -(*MolCenter);
+          SideH = runner->second.second->getPosition() -(*MolCenter);
           SideH.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideH: " << SideH << endl;
@@ -701 +705 @@
   // sum up the atomic masses
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      totalmass += (*iter)->type->mass;
+      totalmass += (*iter)->getType()->mass;
   }
   DoLog(0) && (Log() << Verbose(0) << "RESULT: The summed mass is " << setprecision(10) << totalmass << " atomicmassunit." << endl);
@@ -857 +861 @@
 
           // ... and put at new position
-          Inserter = (*iter)->x;
+          Inserter = (*iter)->getPosition();
           if (DoRandomRotation)
             Inserter *= Rotations;
@@ -882 +886 @@
             // copy atom ...
             CopyAtoms[(*iter)->nr] = (*iter)->clone();
-            CopyAtoms[(*iter)->nr]->x = Inserter;
+            (*CopyAtoms[(*iter)->nr]).setPosition(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);
+            DoLog(1) && (Log() << Verbose(1) << "Filling atom " << **iter << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[(*iter)->nr]->getPosition()) << "." << endl);
           } else {
             DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is inner point, within boundary or outside of MaxDistance." << endl);