Changeset 8f4df1 for src/Actions/AnalysisAction

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).

Location:

src/Actions/AnalysisAction

Files:

• MolecularVolumeAction.cpp (modified) (1 diff)
• PairCorrelationAction.cpp (modified) (1 diff)
• PointCorrelationAction.cpp (modified) (1 diff)
• PrincipalAxisSystemAction.cpp (modified) (1 diff)
• SurfaceCorrelationAction.cpp (modified) (1 diff)

src/Actions/AnalysisAction/MolecularVolumeAction.cpp

@@ -60 +60 @@
     LCList = new LinkedCell(mol, 10.);
     config * const configuration = World::getInstance().getConfig();
-    Boundaries *BoundaryPoints = NULL;
     //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);
     FindNonConvexBorder(mol, TesselStruct, LCList, 5., NULL);

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -70 +70 @@
   double BinStart = 0.;
   double BinWidth = 0.;
-  molecule *Boundary = NULL;
   string outputname;
   string binoutputname;

src/Actions/AnalysisAction/PointCorrelationAction.cpp

@@ -71 +71 @@
   double BinStart = 0.;
   double BinWidth = 0.;
-  molecule *Boundary = NULL;
   string outputname;
   string binoutputname;

src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

@@ -62 +62 @@
     // sum up inertia tensor
     for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      Vector x = (*iter)->x;
+      Vector x = (*iter)->getPosition();
       x -= *CenterOfGravity;
-      InertiaTensor.at(0,0) += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
-      InertiaTensor.at(0,1) += (*iter)->type->mass*(-x[0]*x[1]);
-      InertiaTensor.at(0,2) += (*iter)->type->mass*(-x[0]*x[2]);
-      InertiaTensor.at(1,0) += (*iter)->type->mass*(-x[1]*x[0]);
-      InertiaTensor.at(1,1) += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
-      InertiaTensor.at(1,2) += (*iter)->type->mass*(-x[1]*x[2]);
-      InertiaTensor.at(2,0) += (*iter)->type->mass*(-x[2]*x[0]);
-      InertiaTensor.at(2,1) += (*iter)->type->mass*(-x[2]*x[1]);
-      InertiaTensor.at(2,2) += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
+      const double mass = (*iter)->getType()->mass;
+      InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
+      InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);
+      InertiaTensor.at(0,2) += mass*(-x[0]*x[2]);
+      InertiaTensor.at(1,0) += mass*(-x[1]*x[0]);
+      InertiaTensor.at(1,1) += mass*(x[0]*x[0] + x[2]*x[2]);
+      InertiaTensor.at(1,2) += mass*(-x[1]*x[2]);
+      InertiaTensor.at(2,0) += mass*(-x[2]*x[0]);
+      InertiaTensor.at(2,1) += mass*(-x[2]*x[1]);
+      InertiaTensor.at(2,2) += mass*(x[0]*x[0] + x[1]*x[1]);
     }
     // print InertiaTensor for debugging

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -111 +111 @@
   // find biggest molecule
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
-  int counter  = molecules.size();
   LCList = new LinkedCell(Boundary, LCWidth);
   FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);