Changeset 35a25a for src

Timestamp:

Oct 12, 2011, 2:10:48 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:

220cf64

Parents:

b60804

git-author:

Frederik Heber <heber@…> (10/12/11 13:00:32)

git-committer:

Frederik Heber <heber@…> (10/12/11 14:10:48)

Message:

AtomInfo does not store ref to element anymore but only atomic number.

• if we want to allow for elements to be changed, no refs may be stored at other places. Now we just store the atomic number and look up the element in the periodentafel on request.

Location:

src

Files:

• atom_atominfo.cpp (modified) (5 diffs)
• atom_atominfo.hpp (modified) (2 diffs)

src/atom_atominfo.cpp

@@ -35 +35 @@
  */
 AtomInfo::AtomInfo() :
-  AtomicElement(NULL),
+  AtomicElement(-1),
   FixedIon(false)
 {
@@ -60 +60 @@
 
 AtomInfo::AtomInfo(const VectorInterface &_v) :
-    AtomicElement(NULL),
+    AtomicElement(-1),
     FixedIon(false)
 {
@@ -89 +89 @@
 const element *AtomInfo::getType() const
 {
-  return AtomicElement;
+  const element *elem = World::getInstance().getPeriode()->FindElement(AtomicElement);
+  ASSERT(elem != NULL,
+      "AtomInfo::getType() - there is not element stored under Z="+
+      toString(AtomicElement)+" in the periodentafel.");
+  return elem;
 }
 
@@ -150 +154 @@
 void AtomInfo::setType(const element* _type)
 {
-  OBSERVE;
-  NOTIFY(AtomObservable::ElementChanged);
-  AtomicElement = _type;
+  if (_type->getNumber() != AtomicElement) {
+    OBSERVE;
+    NOTIFY(AtomObservable::ElementChanged);
+    AtomicElement = _type->getNumber();
+  }
 }
 
 void AtomInfo::setType(const int Z)
 {
-  OBSERVE;
-  NOTIFY(AtomObservable::ElementChanged);
   const element *elem = World::getInstance().getPeriode()->FindElement(Z);
-  setType(elem);
+  if (elem != NULL) {
+    OBSERVE;
+    NOTIFY(AtomObservable::ElementChanged);
+    AtomicElement = Z;
+  }
 }
 
@@ -508 +516 @@
 }
 
-double AtomInfo::getMass() const{
-  return AtomicElement->getMass();
+double AtomInfo::getMass() const
+{
+  return getType()->getMass();
 }
 

src/atom_atominfo.hpp

@@ -22 +22 @@
 
 #include "atom_observable.hpp"
+
+#include "types.hpp"
 
 #include "LinearAlgebra/Vector.hpp"
@@ -263 +265 @@
 
 private:
-  const element *AtomicElement;  //!< pointing to element
+  atomicNumber_t AtomicElement;          //!< contains atomic number (i.e. Z of element) or "-1" if unset
   bool FixedIon;
 };