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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC

# Line 1 | Line 1
1   #ifndef _ATOM_H_
2   #define _ATOM_H_
3  
4 < #include <cstring>
5 < #include <cstdlib>
4 > #include <string.h>
5 > #include <stdlib.h>
6   #include <iostream>
7  
8   #include "SimState.hpp"
# Line 13 | Line 13 | class Atom{ (public)
13    Atom(int theIndex, SimState* theConfig );
14    virtual ~Atom() {}
15  
16 <  void setCoords(void);
16 >  virtual void setCoords(void);
17  
18 – //   void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
19 – //                 double* Atrq, double* AAmat, double* Amu,
20 – //                 double* Aul);
21 – //   void deleteAtom(int theIndex);
22 – //   void deleteRange(int startIndex, int stopIndex);
23 –
18    void getPos( double theP[3] );
19    void setPos( double theP[3] );
20  
# Line 69 | Line 63 | class Atom{ (public)
63    void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
64    int isLJ( void )    { return is_LJ; }
65  
66 <  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
66 >  void setVDW( void )        { is_VDW = 1; is_LJ = 0; }
67    int isVDW( void )    { return is_VDW; }
68  
69    void setEAM( void ) { is_EAM = 1; }
70    int  isEAM( void ) { return is_EAM; }
71  
72 +  void setCharged( void ) { is_charged = 1; }
73 +  int isCharged( void ) { return is_charged; }
74 +
75    virtual int isDirectional( void ) = 0;
76  
77  
# Line 111 | Line 108 | class Atom{ (public)
108    int c_n_hyd; // the number of hydrogens bonded to the atom
109    
110    int has_dipole; // dipole boolean
111 <  int is_VDW;    // VDW boolean
112 <  int is_LJ;    // LJ boolean
113 <  int is_EAM; //EAM boolean
111 >  int is_VDW;     // VDW boolean
112 >  int is_LJ;      // LJ boolean
113 >  int is_EAM;     // EAM boolean
114 >  int is_charged;   // isCharge boolean
115  
116    bool hasCoords;
117  
# Line 143 | Line 141 | class DirectionalAtom : public Atom { (public)
141      sux = 0.0;
142      suy = 0.0;
143      suz = 0.0;
144 +    myMu = 0.0;
145    }
146    virtual ~DirectionalAtom() {}
147  
148 +  virtual void setCoords(void);
149 +
150    void printAmatIndex( void );
151  
152    int isDirectional(void) { return 1; }
# Line 215 | Line 216 | class DirectionalAtom : public Atom { (public)
216    void body2Lab( double r[3] );
217  
218  
219 +  // Four functions added for derivatives with respect to Euler Angles:
220 +  // (Needed for minimization routines):
221 +
222 +  void getGrad(double gradient[6] );
223 +  void getEulerAngles( double myEuler[3] );
224 +
225 +  double max(double x, double y);
226 +  double min(double x, double y);
227 +  
228 +
229   private:
230    int dIndex;
231  
232 +  double myMu;
233 +
234    double sux, suy, suz; // the standard unit vector    ( body fixed )
235    double jx, jy, jz;    // the angular momentum vector ( body fixed )
236    

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