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

File:

• src/atom.hpp (modified) (4 diffs)

src/atom.hpp

@@ -11 +11 @@
 using namespace std;
 
+/*********************************************** includes ***********************************/
+
 // include config.h
 #ifdef HAVE_CONFIG_H
@@ -16 +18 @@
 #endif
 
+#include <iostream>
+#include <vector>
 
-#include <iostream>
+#include "tesselation.hpp"
 
-#include "element.hpp"
-#include "tesselation.hpp"
-#include "vector.hpp"
+/****************************************** forward declarations *****************************/
+
+class bond;
+class element;
+class Vector;
+
+/********************************************** declarations *******************************/
 
 /** Single atom.
@@ -28 +36 @@
 class atom : public TesselPoint {
   public:
-    Vector x;       //!< coordinate array of atom, giving position within cell
-    Vector v;       //!< velocity array of atom
+    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
     element *type;  //!< pointing to element
     atom *previous; //!< previous atom in molecule list
@@ -51 +67 @@
   virtual ~atom();
 
-  bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
+  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 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);