Changeset 9df680 for src/atom.cpp

Timestamp:

Feb 3, 2011, 9:51:18 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, Candidate_v1.7.0, 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:

ea430a

Parents:

d6f886

git-author:

Frederik Heber <heber@…> (01/15/11 15:04:18)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:18)

Message:

FIX: FillVoidWithMolecule() now centers filler molecule at its center of gravity.

• this is the only sensible option if we later rotate the molecule.
• atom::clone() reduced a lot, as copy constructors contains it all.
• FillVoidWithMolecule() - filler is now selected to reside entirely within the domain. Otherwise, we seg'fault on save on exit, as one of the father atoms for all copied atoms is missing and hence, we cannot look at its additional...Data for various parsers.
• new function molecule::removeAtomsInMolecule() which destroys all the molecule's atoms.

TESTFIXES:

• Filling/3: filled water box has changed due to different center of water molecules.

File:

• src/atom.cpp (modified) (2 diffs)

src/atom.cpp

@@ -49 +49 @@
     ParticleInfo(pointer),
     father(pointer),
-    sort(&nr)
+    sort(&nr),
+    mol(0)
 {
   setType(pointer->getType());  // copy element of atom
@@ -55 +56 @@
   AtomicVelocity = pointer->AtomicVelocity; // copy velocity
   FixedIon = pointer->FixedIon;
-  mol = 0;
 };
 
 atom *atom::clone(){
   atom *res = new atom(this);
-  res->father = this;
-  res->sort = &res->nr;
-  res->setType(getType());
-  res->setPosition(this->getPosition());
-  res->AtomicVelocity = this->AtomicVelocity;
-  res->FixedIon = FixedIon;
-  res->mol = 0;
   World::getInstance().registerAtom(res);
   return res;