Changes in src/atom.hpp [49f802c:055861]

File:

• src/atom.hpp (modified) (4 diffs)

src/atom.hpp

@@ -11 +11 @@
 using namespace std;
 
-/*********************************************** includes ***********************************/
-
 // include config.h
 #ifdef HAVE_CONFIG_H
@@ -18 +16 @@
 #endif
 
+
 #include <iostream>
-#include <vector>
 
+#include "element.hpp"
 #include "tesselation.hpp"
-
-/****************************************** forward declarations *****************************/
-
-class bond;
-class element;
-class Vector;
-
-/********************************************** declarations *******************************/
+#include "vector.hpp"
 
 /** Single atom.
@@ -36 +28 @@
 class atom : public TesselPoint {
   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
+    Vector x;       //!< coordinate array of atom, giving position within cell
+    Vector v;       //!< velocity array of atom
     element *type;  //!< pointing to element
     atom *previous; //!< previous atom in molecule list
@@ -67 +51 @@
   virtual ~atom();
 
-  bool Output(ofstream *out, int ElementNo, int AtomNo, const char *comment = NULL) const;
-  bool Output(ofstream *out, int *ElementNo, int *AtomNo, const char *comment = NULL);
+  bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
   bool OutputXYZLine(ofstream *out) const;
-  bool OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const;
-  bool OutputTrajectoryXYZ(ofstream *out, int step) const;
-  bool OutputBondOfAtom(ofstream *out, int *NumberOfBondsPerAtom, bond ***ListOfBondsPerAtom) const;
-
-  void EqualsFather ( atom *ptr, atom **res );
-  void CorrectFather();
   atom *GetTrueFather();
   bool Compare(const atom &ptr);
-
-  double DistanceToVector(Vector &origin);
-  double DistanceSquaredToVector(Vector &origin);
-
-  void AddKineticToTemperature(double *temperature, int step) const;
-
-  bool IsInParallelepiped(Vector offset, double *parallelepiped);
 
   ostream & operator << (ostream &ost);