Changeset a1c8fa for src/Atom

Timestamp:

Oct 20, 2016, 8:54:23 PM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChronosMutex, Fix_ForceAnnealing, Fix_ParseParticles, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

72e40d0

Parents:

064b34

git-author:

Frederik Heber <heber@…> (09/27/16 09:58:43)

git-committer:

Frederik Heber <heber@…> (10/20/16 20:54:23)

Message:

FIX: BondedParticleInfo::MaxOrder and ::AdapativeOrder are now stored per trajectory step.

• adapted uses in AdaptivityMap and Fragmentation as members are now protected.

Location:

src/Atom

Files:

• atom_bondedparticle.cpp (modified) (1 diff)
• atom_bondedparticleinfo.cpp (modified) (2 diffs)
• atom_bondedparticleinfo.hpp (modified) (4 diffs)

src/Atom/atom_bondedparticle.cpp

@@ -71 +71 @@
 void BondedParticle::OutputOrder(ofstream *file) const
 {
-  *file << getNr() << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
-  //LOG(2, "Storing: " << getNr() << "\t" << (int)AdaptiveOrder << "\t" << MaxOrder << ".");
+  *file << getNr() << "\t" << (int)getAdaptiveOrder() << "\t" << (int)getMaxOrder() << endl;
+  //LOG(2, "Storing: " << getNr() << "\t" << (int)getAdaptiveOrder() << "\t" << getMaxOrder() << ".");
 };
 

src/Atom/atom_bondedparticleinfo.cpp

@@ -45 +45 @@
 BondList BondedParticleInfo::emptyList;
 
-/** Constructor of class BondedParticleInfo.
- */
-BondedParticleInfo::BondedParticleInfo() :
-  AdaptiveOrder(0),
-  MaxOrder(0)
-{}
-
-/** Destructor of class BondedParticleInfo.
- */
-BondedParticleInfo::~BondedParticleInfo()
-{}
-
 void BondedParticleInfo::AppendTrajectoryStep(const unsigned int _step)
 {
@@ -74 +62 @@
 }
 
+template <class List_t>
+void setEntryInList(
+    List_t &_list,
+    const typename List_t::key_type _step,
+    const typename List_t::mapped_type &_value)
+{
+  typename List_t::iterator iter =
+    _list.find(_step);
+  if (iter != _list.end())
+    iter->second = _value;
+  else
+    _list.insert( std::make_pair(_step, _value) );
+}
+
+template <class List_t>
+const typename List_t::mapped_type& getEntryInList(
+    const List_t &_list,
+    const typename List_t::key_type _step,
+    const typename List_t::mapped_type &_empty)
+{
+  typename List_t::const_iterator iter =
+    _list.find(_step);
+  if (iter != _list.end())
+    return iter->second;
+  return _empty;
+}
+
 const BondList& BondedParticleInfo::getListOfBondsAtStep(unsigned int _step) const
 {
-  BondTrajectory_t::const_iterator iter =
-    ListOfBonds.find(_step);
-  if (iter != ListOfBonds.end())
-    return iter->second;
-  return emptyList;
+  return getEntryInList<BondTrajectory_t>(ListOfBonds, _step, emptyList);
 }
+
+const unsigned char& BondedParticleInfo::getMaxOrder() const
+{
+  return getMaxOrder(WorldTime::getTime());
+}
+
+const unsigned char& BondedParticleInfo::getMaxOrder(unsigned int _step) const
+{
+  static unsigned char emptyOrder=0;
+  return getEntryInList<OrderTrajectory_t>(MaxOrder, _step, emptyOrder);
+}
+
+void BondedParticleInfo::setMaxOrder(unsigned char _value)
+{
+  setMaxOrder(WorldTime::getTime(), _value);
+}
+
+void BondedParticleInfo::setMaxOrder(unsigned int _step, const unsigned char _value)
+{
+  setEntryInList<OrderTrajectory_t>(MaxOrder, _step, _value);
+}
+
+const unsigned char& BondedParticleInfo::getAdaptiveOrder() const
+{
+  return getAdaptiveOrder(WorldTime::getTime());
+}
+
+const unsigned char& BondedParticleInfo::getAdaptiveOrder(unsigned int _step) const
+{
+  static unsigned char emptyOrder=0;
+  return getEntryInList<OrderTrajectory_t>(AdaptiveOrder, _step, emptyOrder);
+}
+
+void BondedParticleInfo::setAdaptiveOrder(unsigned char _value)
+{
+  setAdaptiveOrder(WorldTime::getTime(), _value);
+}
+
+void BondedParticleInfo::setAdaptiveOrder(unsigned int _step, const unsigned char _value)
+{
+  setEntryInList<OrderTrajectory_t>(AdaptiveOrder, _step, _value);
+}
+

src/Atom/atom_bondedparticleinfo.hpp

@@ -37 +37 @@
   friend class BondedParticle;
 public:
-  unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
-  unsigned char MaxOrder;  //!< desired maximum order of this atom (0 means "not set")
 
-  BondedParticleInfo();
-  virtual ~BondedParticleInfo();
+  virtual ~BondedParticleInfo() {}
 
   /** Pushes back another step in all trajectory vectors.
@@ -65 +62 @@
   const BondList& getListOfBonds() const;
 
-  /** Accessor to ListOfBonds of WorldTime::CurrentTime.
-   *
-   * Note, new empty BondList is returned if array entry at upper boundary is
-   * accessed. Beyond std will issue exception due to out-of-range access.
-   *
-   * @return ListOfBonds[WorldTime::CurrentTime]
-   */
-//  BondList& getListOfBonds();
-
   /** Const Accessor ListOfBonds of any present time step.
    *
@@ -81 +69 @@
   const BondList& getListOfBondsAtStep(unsigned int _step) const;
 
-  /** Accessor ListOfBonds of any present time step.
+  /** Const getter for the MaxOrder property at current time step.
    *
-   * Note, new empty BondList is returned if array entry at upper boundary is
-   * accessed. Beyond std will issue exception due to out-of-range access.
+   * @return MaxOrder[Current world time step].
+   */
+  const unsigned char& getMaxOrder() const;
+
+  /** Const getter for the MaxOrder property at given \a _step.
    *
    * @param _step time step to access
-   * @return ListOfBonds[_step].
+   * @return MaxOrder[_step].
    */
-//  BondList& getListOfBondsAtStep(unsigned int _step);
+  const unsigned char& getMaxOrder(const unsigned int _step) const;
+
+  /** Setter for the MaxOrder property at current time step.
+   *
+   * @param _value value to set for MaxOrder at current time step
+   */
+  void setMaxOrder(const unsigned char _value);
+
+  /**Setter for the MaxOrder property at given \a _step.
+   *
+   * @param _step time step to access
+   * @param _value value to set for MaxOrder at the desired time step
+   * @return MaxOrder[_step].
+   */
+  void setMaxOrder(const unsigned int _step, const unsigned char _value);
+
+  /** Const getter for the AdaptiveOrder property at current time step.
+   *
+   * @return AdaptiveOrder[Current world time step].
+   */
+  const unsigned char& getAdaptiveOrder() const;
+
+  /** Const getter for the AdaptiveOrder property at given \a _step.
+   *
+   * @param _step time step to access
+   * @return AdaptiveOrder[_step].
+   */
+  const unsigned char& getAdaptiveOrder(const unsigned int _step) const;
+
+  /** Setter for the AdaptiveOrder property at current time step.
+   *
+   * @param _value value to set for AdaptiveOrder at current time step
+   */
+  void setAdaptiveOrder(const unsigned char _value);
+
+  /** Setter for the AdaptiveOrder property at given \a _step.
+   *
+   * @param _step time step to access
+   * @param _value value to set for AdaptiveOrder at the desired time step
+   * @return AdaptiveOrder[_step].
+   */
+  void setAdaptiveOrder(const unsigned int _step, const unsigned char _value);
 
 protected:
@@ -105 +137 @@
   BondTrajectory_t ListOfBonds; //!< list of all bonds
   static BondList emptyList;  //!< empty list to return when step is not present
+
+  typedef std::map<unsigned int, unsigned char> OrderTrajectory_t;
+  OrderTrajectory_t AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
+  OrderTrajectory_t MaxOrder;  //!< desired maximum order of this atom (0 means "not set")
 };