Changeset 560bbe for src/Atom

Timestamp:

Feb 17, 2012, 3:24:18 PM (13 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:

cdaae6

Parents:

ac5c36

git-author:

Frederik Heber <heber@…> (01/06/12 16:49:11)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:18)

Message:

AtomicInfo now also (re)stores ParticleInfo::Nr, molecule has own IdPool.

• molecule now also has an internal IdPool to be able to hand out unique ids, according to uniqueId policy.
• new functions: molecule::changeAtomNr(), molecule::setAtomName()
• molecule::erase() and ::insert() release and set the id (and the name).
• molecule::setAtomName() uses getNr() with id increased by one.
• AtomicInfo stores and sets ParticleInfo::Nr.
• atom::changeNr() is similar to changeId() only for the molecule.
• molecule::AddAtom() does not set the name anymore, is done by ::insert().
• simplified molecule::doCountAtoms() a lot, no more naming of atoms.
• SPEEDUP: This speeds up the GUI already a lot.
• TESTFIX: changed regression test Tesselation/BigNonConvex due to different ordering of node ids (due to above), surface is still the same (checked).

Location:

src/Atom

Files:

• AtomicInfo.cpp (modified) (4 diffs)
• AtomicInfo.hpp (modified) (1 diff)
• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)

src/Atom/AtomicInfo.cpp

@@ -35 +35 @@
     FatherId(0),
     MolId(0),
-    Id(0)
+    Id(0),
+    Nr(0)
 {}
 AtomicInfo::AtomicInfo(const atom &_atom) :
@@ -43 +44 @@
     FatherId(_atom.father->getId()),
     MolId(_atom.getMolecule()->getId()),
-    Id(_atom.getId())
+    Id(_atom.getId()),
+    Nr(_atom.getNr())
 {}
 
@@ -72 +74 @@
   if (_mol != NULL)
     _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
+  _atom.changeNr(Nr);
 
   return status;
@@ -90 +93 @@
   Velocity = AI.Velocity;
   Id = AI.Id;
+  Nr = AI.Nr;
   return *this;
 }

src/Atom/AtomicInfo.hpp

@@ -41 +41 @@
   moleculeId_t MolId;
   atomId_t Id;
+  int Nr;
 };
 

src/Atom/atom.cpp

@@ -322 +322 @@
 }
 
+bool atom::changeNr(const int newNr)
+{
+  if ((mol) && (mol->changeAtomNr(getNr(),newNr,this))) {
+    return true;
+  } else{
+    return false;
+  }
+}
+
 int atom::getNr() const{
   return ParticleInfo::getNr();

src/Atom/atom.hpp

@@ -211 +211 @@
     */
    void removeFromMolecule();
+
+   /** Changes the molecule internal ParticleInfo::Nr of this atom.
+    *
+    * @param newNr new ParticleInfo::Nr to set
+    * @return true - change successful, false - changed not successful, id remains the old one
+    */
+   bool changeNr(int newNr);
 
    /** Getter for ParticleInfo::Nr of the atom.