Changeset 2e2a70 for molecuilder/src/atom.hpp

Timestamp:

Oct 20, 2009, 8:55:17 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

2e6aa1

Parents:

3b0ba2

Message:

Refactored atom.cpp into multiple files.

After the class atom was refactored into multiple base classes that are inherited, these base classes are also all put into separate files. This is basically a preparatory step for the like-wise refactoring of class molecule into inherited base classes and splitting up (that is there done already). Finally, we will also separate the relations, i.e. not have "atom.hpp" included everywhere and use class atom, but rather the subclasses such as TrajectoryParticle and its header files only.
Signed-off-by: Frederik Heber <heber@…>

File:

• molecuilder/src/atom.hpp (modified) (1 diff)

molecuilder/src/atom.hpp

@@ -22 +22 @@
 #include <vector>
 
-#include <gsl/gsl_randist.h>
-
+#include "atom_atominfo.hpp"
+#include "atom_bondedparticle.hpp"
+#include "atom_graphnode.hpp"
+#include "atom_particleinfo.hpp"
+#include "atom_trajectoryparticle.hpp"
 #include "tesselation.hpp"
 
 /****************************************** forward declarations *****************************/
 
-class atom;
-class bond;
-class config;
-class element;
-class ForceMatrix;
 class Vector;
 
-#define BondList list<bond *>
-
 /********************************************** 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.