Changeset 4455f4 for src/atom.hpp

Timestamp:

Oct 19, 2009, 1:09:29 PM (16 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:

c75de1

Parents:

9eefda

Message:

Huge Refactoring: class atom split up into several inherited classes.

• There are now two parts: classes containing data (called ...Info) and classes containing associated functions:
  • new data classes: ParticleInfo (id and name), AtomInfo (element, position, velocity, force), TrajectoryParticleInfo, GraphNodeInfo (all graph variables), BondedParticleInfo (AdaptiveOrder, MaxOrder, ListOfBonds)
  • new associated function classes: TrajectoryParticle, GraphNode, BondedParticle

• template functions ActOnAllAtoms(), SumPerAtom() were adapted with another template type for the class of the member function
• template functions SetIndexedArrayForEachAtomTo() have their index as ParticleInfo::*index

File:

• src/atom.hpp (modified) (4 diffs)

src/atom.hpp

@@ -28 +28 @@
 /****************************************** forward declarations *****************************/
 
+class atom;
 class bond;
 class config;
@@ -38 +39 @@
 /********************************************** declarations *******************************/
 
+class AtomInfo {
+public:
+  Vector x;       //!< coordinate vector of atom, giving last position within cell
+  Vector v;       //!< velocity vector of atom, giving last velocity within cell
+  Vector F;       //!< Force vector of atom, giving last force within cell
+  element *type;  //!< pointing to element
+
+  AtomInfo();
+  ~AtomInfo();
+
+private:
+};
+
+class TrajectoryParticleInfo {
+public:
+  struct
+  {
+    vector<Vector> R;  //!< position vector
+    vector<Vector> U;  //!< velocity vector
+    vector<Vector> F;  //!< last force vector
+  } Trajectory;
+  int FixedIon;   //!< config variable that states whether forces act on the ion or not
+
+  TrajectoryParticleInfo();
+  ~TrajectoryParticleInfo();
+
+private:
+};
+
+class TrajectoryParticle :  public TrajectoryParticleInfo, public virtual AtomInfo, public virtual ParticleInfo {
+public:
+
+  TrajectoryParticle();
+  virtual ~TrajectoryParticle();
+
+  // constraint potential and dynamics stuff
+  void AddKineticToTemperature(double *temperature, int step) const;
+  void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
+  void CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity);
+
+  // trajectory stuff
+  void ResizeTrajectory(int MaxSteps);
+  void CopyStepOnStep(int dest, int src);
+  void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force);
+  void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity );
+
+  // thermostats
+  void Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin);
+  void Thermostat_Gaussian_init(int Step, double *G, double *E);
+  void Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration);
+  void Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration);
+  void Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration);
+  void Thermostat_NoseHoover_init(int Step, double *delta_alpha);
+  void Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration);
+
+private:
+
+};
+
+class GraphNode;
+
+class GraphNodeInfo {
+public:
+
+  int GraphNr;      //!< unique number, given in DepthFirstSearchAnalysis()
+  int *ComponentNr;//!< belongs to this non-separable components, given in DepthFirstSearchAnalysis() (if more than one, then is SeparationVertex)
+  int LowpointNr; //!< needed in DepthFirstSearchAnalysis() to detect non-separable components, is the lowest possible number of an atom to reach via tree edges only followed by at most one back edge.
+  bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, determined in DepthFirstSearchAnalysis()
+  bool IsCyclic;        //!< whether atom belong to as cycle or not, determined in DepthFirstSearchAnalysis()
+  atom *Ancestor; //!< "Father" in Depth-First-Search
+
+  GraphNodeInfo();
+  ~GraphNodeInfo();
+private:
+
+};
+
+
+class GraphNode : public GraphNodeInfo, public virtual ParticleInfo {
+public:
+
+  GraphNode();
+  virtual ~GraphNode();
+
+  void OutputGraphInfo(ofstream *out) const;
+  void OutputComponentNumber(ofstream *out) const;
+
+private:
+
+};
+
+class BondedParticleInfo {
+public:
+  unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
+  bool MaxOrder;  //!< whether this atom as a root in fragmentation still creates more fragments on higher orders or not
+  BondList ListOfBonds; //!< list of all bonds
+
+  BondedParticleInfo();
+  ~BondedParticleInfo();
+
+private:
+
+};
+
+class BondedParticle : public BondedParticleInfo, public virtual ParticleInfo, public virtual AtomInfo {
+public:
+  BondedParticle();
+  virtual ~BondedParticle();
+
+  bool RegisterBond(bond *Binder);
+  bool UnregisterBond(bond *Binder);
+  void UnregisterAllBond();
+  int CountBonds() const;
+  int CorrectBondDegree(ofstream *out);
+  bool OutputBondOfAtom(ofstream *out) const;
+  void OutputAdjacency(ofstream *AdjacencyFile) const;
+  void OutputOrder(ofstream *file);
+
+private:
+
+};
+
 /** Single atom.
  * Class incorporates position, type
  */
-class atom : public TesselPoint {
+class atom : public TesselPoint, public TrajectoryParticle, public GraphNode, public BondedParticle, public virtual ParticleInfo, public virtual AtomInfo {
   public:
-    struct
-    {
-      vector<Vector> R;  //!< position vector
-      vector<Vector> U;  //!< velocity vector
-      vector<Vector> F;  //!< last force vector
-    } Trajectory;
-
-    Vector x;       //!< coordinate vector of atom, giving last position within cell
-    Vector v;       //!< velocity vector of atom, giving last velocity within cell
-    Vector F;       //!< Force vector of atom, giving last force within cell
-    BondList ListOfBonds; //!< list of all bonds
-    element *type;  //!< pointing to element
     atom *previous; //!< previous atom in molecule list
     atom *next;     //!< next atom in molecule list
     atom *father;   //!< In many-body bond order fragmentations points to originating atom
-    atom *Ancestor; //!< "Father" in Depth-First-Search
-    //char *Name;      //!< unique name used during many-body bond-order fragmentation, comes from TesselPoint
-    int FixedIon;   //!< config variable that states whether forces act on the ion or not
     int *sort;      //!< sort criteria
-    //int nr;         //!< continuous, unique number, comes from TesselPoint
-    int GraphNr;      //!< unique number, given in DepthFirstSearchAnalysis()
-    int *ComponentNr;//!< belongs to this nonseparable components, given in DepthFirstSearchAnalysis() (if more than one, then is SeparationVertex)
-    int LowpointNr; //!< needed in DepthFirstSearchAnalysis() to detect nonseparable components, is the lowest possible number of an atom to reach via tree edges only followed by at most one back edge.
-    bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, determined in DepthFirstSearchAnalysis()
-    bool IsCyclic;        //!< whether atom belong to as cycle or not, determined in DepthFirstSearchAnalysis()
-    unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
-    bool MaxOrder;  //!< whether this atom as a root in fragmentation still creates more fragments on higher orders or not
 
   atom();
@@ -80 +180 @@
   bool OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const;
   bool OutputTrajectoryXYZ(ofstream *out, int step) const;
-  bool OutputBondOfAtom(ofstream *out) const;
-  void OutputAdjacency(ofstream *AdjacencyFile) const;
+  void OutputMPQCLine(ofstream *out, Vector *center, int *AtomNo) const;
 
+  void InitComponentNr();
 
   void EqualsFather ( atom *ptr, atom **res );
@@ -89 +189 @@
   bool Compare(const atom &ptr);
 
-  // trajectory stuff
-  void ResizeTrajectory(int MaxSteps);
-  void CopyStepOnStep(int dest, int src);
-  void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force);
-  void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity );
-
   double DistanceToVector(Vector &origin);
   double DistanceSquaredToVector(Vector &origin);
-
   bool IsInParallelepiped(Vector offset, double *parallelepiped);
-
-  // bond order stuff
-  void OutputOrder(ofstream *file);
-  void OutputGraphInfo(ofstream *out) const;
-  void OutputComponentNumber(ofstream *out) const;
-  void InitComponentNr();
-  int CountBonds() const;
-  int CorrectBondDegree(ofstream *out);
-
-  bool RegisterBond(bond *Binder);
-  bool UnregisterBond(bond *Binder);
-  void UnregisterAllBond();
-
-  // constraint potential and dynamics stuff
-  void AddKineticToTemperature(double *temperature, int step) const;
-  void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
-  void CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity);
-
-  // thermostats
-  void Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin);
-  void Thermostat_Gaussian_init(int Step, double *G, double *E);
-  void Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration);
-  void Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration);
-  void Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration);
-  void Thermostat_NoseHoover_init(int Step, double *delta_alpha);
-  void Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration);
-
-
-  ostream & operator << (ostream &ost);
 
   private:
 };
 
-ostream & operator << (ostream &ost, const atom &a);
-
 #endif /* ATOM_HPP_ */