Ignore:
Timestamp:
Aug 7, 2010, 12:07:04 PM (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:
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:
1 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

    r8d6d31 r8f4df1  
    8383    // sum up inertia tensor
    8484    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    85       Vector x = (*iter)->x;
     85      Vector x = (*iter)->getPosition();
    8686      x -= *CenterOfGravity;
    87       InertiaTensor.at(0,0) += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
    88       InertiaTensor.at(0,1) += (*iter)->type->mass*(-x[0]*x[1]);
    89       InertiaTensor.at(0,2) += (*iter)->type->mass*(-x[0]*x[2]);
    90       InertiaTensor.at(1,0) += (*iter)->type->mass*(-x[1]*x[0]);
    91       InertiaTensor.at(1,1) += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
    92       InertiaTensor.at(1,2) += (*iter)->type->mass*(-x[1]*x[2]);
    93       InertiaTensor.at(2,0) += (*iter)->type->mass*(-x[2]*x[0]);
    94       InertiaTensor.at(2,1) += (*iter)->type->mass*(-x[2]*x[1]);
    95       InertiaTensor.at(2,2) += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
     87      const double mass = (*iter)->getType()->mass;
     88      InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
     89      InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);
     90      InertiaTensor.at(0,2) += mass*(-x[0]*x[2]);
     91      InertiaTensor.at(1,0) += mass*(-x[1]*x[0]);
     92      InertiaTensor.at(1,1) += mass*(x[0]*x[0] + x[2]*x[2]);
     93      InertiaTensor.at(1,2) += mass*(-x[1]*x[2]);
     94      InertiaTensor.at(2,0) += mass*(-x[2]*x[0]);
     95      InertiaTensor.at(2,1) += mass*(-x[2]*x[1]);
     96      InertiaTensor.at(2,2) += mass*(x[0]*x[0] + x[1]*x[1]);
    9697    }
    9798    // print InertiaTensor for debugging
    … …  
    121122
    122123    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    123       *((*iter)->node) -= *CenterOfGravity;
    124       *((*iter)->node) = RotationAxis.rotateVector(*((*iter)->node), alpha);
    125       *((*iter)->node) += *CenterOfGravity;
     124      *(*iter) -= *CenterOfGravity;
     125      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), alpha));
     126      *(*iter) += *CenterOfGravity;
    126127    }
    127128    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
    … …  
    133134    // sum up inertia tensor
    134135    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    135       Vector x = (*iter)->x;
     136      Vector x = (*iter)->getPosition();
    136137      x -= *CenterOfGravity;
    137       InertiaTensor.at(0,0) += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
    138       InertiaTensor.at(0,1) += (*iter)->type->mass*(-x[0]*x[1]);
    139       InertiaTensor.at(0,2) += (*iter)->type->mass*(-x[0]*x[2]);
    140       InertiaTensor.at(1,0) += (*iter)->type->mass*(-x[1]*x[0]);
    141       InertiaTensor.at(1,1) += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
    142       InertiaTensor.at(1,2) += (*iter)->type->mass*(-x[1]*x[2]);
    143       InertiaTensor.at(2,0) += (*iter)->type->mass*(-x[2]*x[0]);
    144       InertiaTensor.at(2,1) += (*iter)->type->mass*(-x[2]*x[1]);
    145       InertiaTensor.at(2,2) += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
     138      const double mass = (*iter)->getType()->mass;
     139      InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
     140      InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);
     141      InertiaTensor.at(0,2) += mass*(-x[0]*x[2]);
     142      InertiaTensor.at(1,0) += mass*(-x[1]*x[0]);
     143      InertiaTensor.at(1,1) += mass*(x[0]*x[0] + x[2]*x[2]);
     144      InertiaTensor.at(1,2) += mass*(-x[1]*x[2]);
     145      InertiaTensor.at(2,0) += mass*(-x[2]*x[0]);
     146      InertiaTensor.at(2,1) += mass*(-x[2]*x[1]);
     147      InertiaTensor.at(2,2) += mass*(x[0]*x[0] + x[1]*x[1]);
    146148      // print InertiaTensor for debugging
    147149      DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << InertiaTensor << endl);
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